CudaSPONGE高性能GPU分子模拟
技术背景CudaSPONGE是基于CUDA C开发的一款纯GPU分子动力学模拟软件，具有模块化和高性能的特点。官方基本介绍内容如下：
分子动力学（Molecular Dynamics, MD）模拟是化学、物理学、生物学、材料科学和许多其他领域的有用工具。在过去 40 年中，人们开发了各种高效的计算算法和MD程序，用于研究日益复杂和大型系统的动力学，如RNA 聚合酶、细胞膜中的膜蛋白、SARS-CoV-2病毒等。然而，随着应用范围和规模的扩大，分子模拟软件需要更高的计算能力。缩小模拟与实验之间差距的最直接策略是利用更强大的计算硬件。例如，Shaw研究所专门设计了安东（Anton），可以对系统大小为几百万个原子的单结构域蛋白质进行毫秒级模拟。相比之下，使用图形处理单元（GPU）可能是大多数研究小组最经济实惠和最有前途的方法。从另一个方面看，许多先进的计算算法也已开发出来并得到广泛应用，从而延长了模拟时间尺度。特别是在过去几十年中，人们开发了许多增强型采样方法，以实现快速热力学和/或动力学计算。这些方法包括但不限于广泛使用的伞状采样、元动力学、加速MD、复制交换分子动力学（REMD）、并行回火、模拟回火、多正则模拟（特别是通过Wang-Landau算法实现）以及许多其他方法。
在过去的 15 年中，我们致力于开发面向复杂化学和生物系统的高效分子模拟方法，设计了一系列增强型采样方法，实现了构象和轨迹空间的快速采样，并实现了复杂系统热力学和动力学特性的快速计算。 最近，我们开发了一个名为 SPONGE的国产MD模拟软件包，它不仅实现了GPU加速的传统MD模拟，还实现了我们课题组提出的高效增强采样方法。 该软件包具有高度模块化的特点，可以轻松集成其他功能或算法，尤其是最新的深度学习潜力和算法。
安装介绍
首先进到CudaSPONGE官网，找到最新版本的软件包下载到本地目录，主要依赖于nvcc进行编译构建。解包之后可以看到这样的目录：
$ lltotal 220drwxrwxrwx 1 root root4096 Sep 11 08:19 ./drwxrwxrwx 1 root root4096 Sep 11 08:19 ../drwxrwxrwx 1 root root4096 Sep 11 08:19 Lennard_Jones_force/drwxrwxrwx 1 root root4096 Sep 11 08:19 MD_core/-rwxrwxrwx 1 root root3072 Jan12024 Makefile*drwxrwxrwx 1 root root4096 Sep 11 08:19 No_PBC/drwxrwxrwx 1 root root4096 Sep 11 08:19 PME_force/drwxrwxrwx 1 root root4096 Sep 11 08:19 SITS/drwxrwxrwx 1 root root4096 Sep 11 08:19 angle/drwxrwxrwx 1 root root4096 Sep 11 08:19 barostats/drwxrwxrwx 1 root root4096 Sep 11 08:19 bias/drwxrwxrwx 1 root root4096 Sep 11 08:19 bond/drwxrwxrwx 1 root root4096 Sep 11 08:19 cmap/drwxrwxrwx 1 root root4096 Sep 11 08:19 collective_variable/-rwxrwxrwx 1 root root8311 Jan12024 common.cu*-rwxrwxrwx 1 root root 58097 Jan12024 common.cuh*drwxrwxrwx 1 root root4096 Sep 11 08:19 constrain/-rwxrwxrwx 1 root root 41504 Jan12024 control.cu*-rwxrwxrwx 1 root root9465 Jan12024 control.cuh*drwxrwxrwx 1 root root4096 Sep 11 08:19 covid-tip4p/drwxrwxrwx 1 root root4096 Sep 11 08:19 dihedral/-rwxrwxrwx 1 root root 34743 Jan12024 jit.cuh*-rwxrwxrwx 1 root root 32719 Jan12024 main.cu*-rwxrwxrwx 1 root root2011 Jan12024 main.cuh*-rwxrwxrwx 1 root root3408 Jan12024 main_ti.cu*-rwxrwxrwx 1 root root 489 Jan12024 main_ti.cuh*-rwxrwxrwx 1 root root 492 Jan12024 mdin.txt*drwxrwxrwx 1 root root4096 Sep 11 08:19 nb14/drwxrwxrwx 1 root root4096 Sep 11 08:19 neighbor_list/drwxrwxrwx 1 root root4096 Sep 11 08:19 plugin/drwxrwxrwx 1 root root4096 Sep 11 08:19 restrain/drwxrwxrwx 1 root root4096 Sep 11 08:19 thermostats/drwxrwxrwx 1 root root4096 Sep 11 08:19 virtual_atoms/-rwxrwxrwx 1 root root 11843 Jan12024 vs_project_generator.bat*drwxrwxrwx 1 root root4096 Sep 11 08:19 wall/然后可以在这个路径下直接执行：
$ make过程中大致输出为：
编译输出$ make/bin/sh: bc: command not found/bin/sh: bc: command not foundanalyzing dependency of PME_force/cross_PME.cu to PME_force/cross_PME.danalyzing dependency of PME_force/PME_force.cu to PME_force/PME_force.danalyzing dependency of Lennard_Jones_force/LJ_soft_core.cu to Lennard_Jones_force/LJ_soft_core.danalyzing dependency of neighbor_list/neighbor_list.cu to neighbor_list/neighbor_list.danalyzing dependency of MD_core/MD_core.cu to MD_core/MD_core.danalyzing dependency of control.cu to control.danalyzing dependency of common.cu to common.danalyzing dependency of main_ti.cu to main_ti.danalyzing dependency of plugin/plugin.cu to plugin/plugin.danalyzing dependency of wall/soft_wall.cu to wall/soft_wall.danalyzing dependency of wall/hard_wall.cu to wall/hard_wall.danalyzing dependency of bias/Meta1D.cu to bias/Meta1D.danalyzing dependency of bias/steer.cu to bias/steer.danalyzing dependency of bias/restrain_cv.cu to bias/restrain_cv.danalyzing dependency of collective_variable/combine.cu to collective_variable/combine.danalyzing dependency of collective_variable/tabulated.cu to collective_variable/tabulated.danalyzing dependency of collective_variable/RMSD.cu to collective_variable/RMSD.danalyzing dependency of collective_variable/simple_cv.cu to collective_variable/simple_cv.danalyzing dependency of collective_variable/collective_variable.cu to collective_variable/collective_variable.danalyzing dependency of SITS/SITS.cu to SITS/SITS.danalyzing dependency of virtual_atoms/virtual_atoms.cu to virtual_atoms/virtual_atoms.danalyzing dependency of constrain/SHAKE.cu to constrain/SHAKE.danalyzing dependency of constrain/SETTLE.cu to constrain/SETTLE.danalyzing dependency of constrain/simple_constrain.cu to constrain/simple_constrain.danalyzing dependency of constrain/constrain.cu to constrain/constrain.danalyzing dependency of restrain/restrain.cu to restrain/restrain.danalyzing dependency of barostats/andersen_barostat.cu to barostats/andersen_barostat.danalyzing dependency of barostats/Berendsen_barostat.cu to barostats/Berendsen_barostat.danalyzing dependency of barostats/MC_barostat.cu to barostats/MC_barostat.danalyzing dependency of thermostats/nose_hoover_chain.cu to thermostats/nose_hoover_chain.danalyzing dependency of thermostats/Berendsen_thermostat.cu to thermostats/Berendsen_thermostat.danalyzing dependency of thermostats/Andersen_thermostat.cu to thermostats/Andersen_thermostat.danalyzing dependency of thermostats/Middle_Langevin_MD.cu to thermostats/Middle_Langevin_MD.danalyzing dependency of thermostats/Langevin_MD.cu to thermostats/Langevin_MD.danalyzing dependency of Lennard_Jones_force/pairwise_force.cu to Lennard_Jones_force/pairwise_force.danalyzing dependency of Lennard_Jones_force/solvent_LJ.cu to Lennard_Jones_force/solvent_LJ.danalyzing dependency of Lennard_Jones_force/Lennard_Jones_force.cu to Lennard_Jones_force/Lennard_Jones_force.danalyzing dependency of No_PBC/Lennard_Jones_force_No_PBC.cu to No_PBC/Lennard_Jones_force_No_PBC.danalyzing dependency of No_PBC/generalized_Born.cu to No_PBC/generalized_Born.danalyzing dependency of No_PBC/Coulomb_Force_No_PBC.cu to No_PBC/Coulomb_Force_No_PBC.danalyzing dependency of nb14/nb14.cu to nb14/nb14.danalyzing dependency of cmap/cmap.cu to cmap/cmap.danalyzing dependency of dihedral/improper_dihedral.cu to dihedral/improper_dihedral.danalyzing dependency of dihedral/dihedral.cu to dihedral/dihedral.danalyzing dependency of angle/Urey_Bradley_force.cu to angle/Urey_Bradley_force.danalyzing dependency of angle/angle.cu to angle/angle.danalyzing dependency of bond/listed_forces.cu to bond/listed_forces.danalyzing dependency of bond/bond_soft.cu to bond/bond_soft.danalyzing dependency of bond/bond.cu to bond/bond.danalyzing dependency of main.cu to main.d/bin/sh: bc: command not found/bin/sh: bc: command not foundnvcc -o main.o -c main.cu -rdc=true -lcudadevrt -lcuda -lcudart -lcufft -lnvrtc --use_fast_math -O4 -ldl -std=c++11 -arch=sm_50 -DCUDA_ARCH_BIN=50nvcc -o common.o -c common.cu -rdc=true -lcudadevrt -lcuda -lcudart -lcufft -lnvrtc --use_fast_math -O4 -ldl -std=c++11 -arch=sm_50 -DCUDA_ARCH_BIN=50nvcc -o control.o -c control.cu -rdc=true -lcudadevrt -lcuda -lcudart -lcufft -lnvrtc --use_fast_math -O4 -ldl -std=c++11 -arch=sm_50 -DCUDA_ARCH_BIN=50nvcc -o MD_core/MD_core.o -c MD_core/MD_core.cu -rdc=true -lcudadevrt -lcuda -lcudart -lcufft -lnvrtc --use_fast_math -O4 -ldl -std=c++11 -arch=sm_50 -DCUDA_ARCH_BIN=50In file included from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/detail/config/config.h:27:0, from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/detail/config.h:23, from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/sort.h:24, from MD_core/MD_core.cu:2:/usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/detail/config/cpp_dialect.h:131:13: warning: Thrust requires at least C++14. C++11 is deprecated but still supported. C++11 support will be removed in a future release. Define THRUST_IGNORE_DEPRECATED_CPP_DIALECT to suppress this message. THRUST_COMPILER_DEPRECATION_SOFT(C++14, C++11); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/local/cuda/bin/../targets/x86_64-linux/include/cub/util_arch.cuh:36:0, from /usr/local/cuda/bin/../targets/x86_64-linux/include/cub/detail/device_synchronize.cuh:19, from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/system/cuda/detail/util.h:36, from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/system/cuda/detail/for_each.h:35, from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/system/detail/adl/for_each.h:42, from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/detail/for_each.inl:27, from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/for_each.h:277, from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/system/detail/generic/transform.inl:19, from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/system/detail/generic/transform.h:104, from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/detail/transform.inl:27, from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/transform.h:721, from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/system/detail/generic/reduce_by_key.inl:31, from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/system/detail/generic/reduce_by_key.h:87, from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/detail/reduce.inl:28, from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/reduce.h:781, from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/system/detail/generic/find.inl:19, from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/system/detail/generic/find.h:61, from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/detail/find.inl:25, from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/find.h:381, from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/system/detail/generic/sort.inl:26, from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/system/detail/generic/sort.h:152, from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/detail/sort.inl:26, from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/sort.h:1358, from MD_core/MD_core.cu:2:/usr/local/cuda/bin/../targets/x86_64-linux/include/cub/util_cpp_dialect.cuh:142:13: warning: CUB requires at least C++14. C++11 is deprecated but still supported. C++11 support will be removed in a future release. Define CUB_IGNORE_DEPRECATED_CPP_DIALECT to suppress this message. CUB_COMPILER_DEPRECATION_SOFT(C++14, C++11); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/detail/config/config.h:27:0, from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/detail/config.h:23, from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/sort.h:24, from MD_core/MD_core.cu:2:/usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/detail/config/cpp_dialect.h:131:13: warning: Thrust requires at least C++14. C++11 is deprecated but still supported. C++11 support will be removed in a future release. Define THRUST_IGNORE_DEPRECATED_CPP_DIALECT to suppress this message. THRUST_COMPILER_DEPRECATION_SOFT(C++14, C++11); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/local/cuda/bin/../targets/x86_64-linux/include/cub/util_arch.cuh:36:0, from /usr/local/cuda/bin/../targets/x86_64-linux/include/cub/detail/device_synchronize.cuh:19, from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/system/cuda/detail/util.h:36, from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/system/cuda/detail/for_each.h:35, from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/system/detail/adl/for_each.h:42, from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/detail/for_each.inl:27, from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/for_each.h:277, from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/system/detail/generic/transform.inl:19, from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/system/detail/generic/transform.h:104, from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/detail/transform.inl:27, from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/transform.h:721, from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/system/detail/generic/reduce_by_key.inl:31, from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/system/detail/generic/reduce_by_key.h:87, from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/detail/reduce.inl:28, from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/reduce.h:781, from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/system/detail/generic/find.inl:19, from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/system/detail/generic/find.h:61, from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/detail/find.inl:25, from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/find.h:381, from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/system/detail/generic/sort.inl:26, from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/system/detail/generic/sort.h:152, from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/detail/sort.inl:26, from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/sort.h:1358, from MD_core/MD_core.cu:2:/usr/local/cuda/bin/../targets/x86_64-linux/include/cub/util_cpp_dialect.cuh:142:13: warning: CUB requires at least C++14. C++11 is deprecated but still supported. C++11 support will be removed in a future release. Define CUB_IGNORE_DEPRECATED_CPP_DIALECT to suppress this message. CUB_COMPILER_DEPRECATION_SOFT(C++14, C++11); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ nvcc -o bond/bond.o -c bond/bond.cu -rdc=true -lcudadevrt -lcuda -lcudart -lcufft -lnvrtc --use_fast_math -O4 -ldl -std=c++11 -arch=sm_50 -DCUDA_ARCH_BIN=50nvcc -o bond/bond_soft.o -c bond/bond_soft.cu -rdc=true -lcudadevrt -lcuda -lcudart -lcufft -lnvrtc --use_fast_math -O4 -ldl -std=c++11 -arch=sm_50 -DCUDA_ARCH_BIN=50nvcc -o bond/listed_forces.o -c bond/listed_forces.cu -rdc=true -lcudadevrt -lcuda -lcudart -lcufft -lnvrtc --use_fast_math -O4 -ldl -std=c++11 -arch=sm_50 -DCUDA_ARCH_BIN=50nvcc -o angle/angle.o -c angle/angle.cu -rdc=true -lcudadevrt -lcuda -lcudart -lcufft -lnvrtc --use_fast_math -O4 -ldl -std=c++11 -arch=sm_50 -DCUDA_ARCH_BIN=50nvcc -o angle/Urey_Bradley_force.o -c angle/Urey_Bradley_force.cu -rdc=true -lcudadevrt -lcuda -lcudart -lcufft -lnvrtc --use_fast_math -O4 -ldl -std=c++11 -arch=sm_50 -DCUDA_ARCH_BIN=50nvcc -o dihedral/dihedral.o -c dihedral/dihedral.cu -rdc=true -lcudadevrt -lcuda -lcudart -lcufft -lnvrtc --use_fast_math -O4 -ldl -std=c++11 -arch=sm_50 -DCUDA_ARCH_BIN=50nvcc -o dihedral/improper_dihedral.o -c dihedral/improper_dihedral.cu -rdc=true -lcudadevrt -lcuda -lcudart -lcufft -lnvrtc --use_fast_math -O4 -ldl -std=c++11 -arch=sm_50 -DCUDA_ARCH_BIN=50nvcc -o cmap/cmap.o -c cmap/cmap.cu -rdc=true -lcudadevrt -lcuda -lcudart -lcufft -lnvrtc --use_fast_math -O4 -ldl -std=c++11 -arch=sm_50 -DCUDA_ARCH_BIN=50nvcc -o nb14/nb14.o -c nb14/nb14.cu -rdc=true -lcudadevrt -lcuda -lcudart -lcufft -lnvrtc --use_fast_math -O4 -ldl -std=c++11 -arch=sm_50 -DCUDA_ARCH_BIN=50nvcc -o neighbor_list/neighbor_list.o -c neighbor_list/neighbor_list.cu -rdc=true -lcudadevrt -lcuda -lcudart -lcufft -lnvrtc --use_fast_math -O4 -ldl -std=c++11 -arch=sm_50 -DCUDA_ARCH_BIN=50In file included from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/detail/config/config.h:27:0, from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/detail/config.h:23, from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/sort.h:24, from neighbor_list/neighbor_list.cu:2:/usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/detail/config/cpp_dialect.h:131:13: warning: Thrust requires at least C++14. C++11 is deprecated but still supported. C++11 support will be removed in a future release. Define THRUST_IGNORE_DEPRECATED_CPP_DIALECT to suppress this message. THRUST_COMPILER_DEPRECATION_SOFT(C++14, C++11); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/local/cuda/bin/../targets/x86_64-linux/include/cub/util_arch.cuh:36:0, from /usr/local/cuda/bin/../targets/x86_64-linux/include/cub/detail/device_synchronize.cuh:19, from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/system/cuda/detail/util.h:36, from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/system/cuda/detail/for_each.h:35, from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/system/detail/adl/for_each.h:42, from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/detail/for_each.inl:27, from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/for_each.h:277, from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/system/detail/generic/transform.inl:19, from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/system/detail/generic/transform.h:104, from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/detail/transform.inl:27, from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/transform.h:721, from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/system/detail/generic/reduce_by_key.inl:31, from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/system/detail/generic/reduce_by_key.h:87, from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/detail/reduce.inl:28, from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/reduce.h:781, from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/system/detail/generic/find.inl:19, from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/system/detail/generic/find.h:61, from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/detail/find.inl:25, from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/find.h:381, from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/system/detail/generic/sort.inl:26, from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/system/detail/generic/sort.h:152, from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/detail/sort.inl:26, from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/sort.h:1358, from neighbor_list/neighbor_list.cu:2:/usr/local/cuda/bin/../targets/x86_64-linux/include/cub/util_cpp_dialect.cuh:142:13: warning: CUB requires at least C++14. C++11 is deprecated but still supported. C++11 support will be removed in a future release. Define CUB_IGNORE_DEPRECATED_CPP_DIALECT to suppress this message. CUB_COMPILER_DEPRECATION_SOFT(C++14, C++11); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/detail/config/config.h:27:0, from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/detail/config.h:23, from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/sort.h:24, from neighbor_list/neighbor_list.cu:2:/usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/detail/config/cpp_dialect.h:131:13: warning: Thrust requires at least C++14. C++11 is deprecated but still supported. C++11 support will be removed in a future release. Define THRUST_IGNORE_DEPRECATED_CPP_DIALECT to suppress this message. THRUST_COMPILER_DEPRECATION_SOFT(C++14, C++11); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/local/cuda/bin/../targets/x86_64-linux/include/cub/util_arch.cuh:36:0, from /usr/local/cuda/bin/../targets/x86_64-linux/include/cub/detail/device_synchronize.cuh:19, from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/system/cuda/detail/util.h:36, from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/system/cuda/detail/for_each.h:35, from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/system/detail/adl/for_each.h:42, from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/detail/for_each.inl:27, from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/for_each.h:277, from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/system/detail/generic/transform.inl:19, from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/system/detail/generic/transform.h:104, from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/detail/transform.inl:27, from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/transform.h:721, from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/system/detail/generic/reduce_by_key.inl:31, from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/system/detail/generic/reduce_by_key.h:87, from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/detail/reduce.inl:28, from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/reduce.h:781, from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/system/detail/generic/find.inl:19, from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/system/detail/generic/find.h:61, from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/detail/find.inl:25, from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/find.h:381, from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/system/detail/generic/sort.inl:26, from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/system/detail/generic/sort.h:152, from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/detail/sort.inl:26, from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/sort.h:1358, from neighbor_list/neighbor_list.cu:2:/usr/local/cuda/bin/../targets/x86_64-linux/include/cub/util_cpp_dialect.cuh:142:13: warning: CUB requires at least C++14. C++11 is deprecated but still supported. C++11 support will be removed in a future release. Define CUB_IGNORE_DEPRECATED_CPP_DIALECT to suppress this message. CUB_COMPILER_DEPRECATION_SOFT(C++14, C++11); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ nvcc -o No_PBC/Coulomb_Force_No_PBC.o -c No_PBC/Coulomb_Force_No_PBC.cu -rdc=true -lcudadevrt -lcuda -lcudart -lcufft -lnvrtc --use_fast_math -O4 -ldl -std=c++11 -arch=sm_50 -DCUDA_ARCH_BIN=50nvcc -o No_PBC/generalized_Born.o -c No_PBC/generalized_Born.cu -rdc=true -lcudadevrt -lcuda -lcudart -lcufft -lnvrtc --use_fast_math -O4 -ldl -std=c++11 -arch=sm_50 -DCUDA_ARCH_BIN=50nvcc -o No_PBC/Lennard_Jones_force_No_PBC.o -c No_PBC/Lennard_Jones_force_No_PBC.cu -rdc=true -lcudadevrt -lcuda -lcudart -lcufft -lnvrtc --use_fast_math -O4 -ldl -std=c++11 -arch=sm_50 -DCUDA_ARCH_BIN=50nvcc -o Lennard_Jones_force/Lennard_Jones_force.o -c Lennard_Jones_force/Lennard_Jones_force.cu -rdc=true -lcudadevrt -lcuda -lcudart -lcufft -lnvrtc --use_fast_math -O4 -ldl -std=c++11 -arch=sm_50 -DCUDA_ARCH_BIN=50nvcc -o Lennard_Jones_force/solvent_LJ.o -c Lennard_Jones_force/solvent_LJ.cu -rdc=true -lcudadevrt -lcuda -lcudart -lcufft -lnvrtc --use_fast_math -O4 -ldl -std=c++11 -arch=sm_50 -DCUDA_ARCH_BIN=50nvcc -o Lennard_Jones_force/LJ_soft_core.o -c Lennard_Jones_force/LJ_soft_core.cu -rdc=true -lcudadevrt -lcuda -lcudart -lcufft -lnvrtc --use_fast_math -O4 -ldl -std=c++11 -arch=sm_50 -DCUDA_ARCH_BIN=50nvcc -o Lennard_Jones_force/pairwise_force.o -c Lennard_Jones_force/pairwise_force.cu -rdc=true -lcudadevrt -lcuda -lcudart -lcufft -lnvrtc --use_fast_math -O4 -ldl -std=c++11 -arch=sm_50 -DCUDA_ARCH_BIN=50nvcc -o PME_force/PME_force.o -c PME_force/PME_force.cu -rdc=true -lcudadevrt -lcuda -lcudart -lcufft -lnvrtc --use_fast_math -O4 -ldl -std=c++11 -arch=sm_50 -DCUDA_ARCH_BIN=50nvcc -o thermostats/Langevin_MD.o -c thermostats/Langevin_MD.cu -rdc=true -lcudadevrt -lcuda -lcudart -lcufft -lnvrtc --use_fast_math -O4 -ldl -std=c++11 -arch=sm_50 -DCUDA_ARCH_BIN=50nvcc -o thermostats/Middle_Langevin_MD.o -c thermostats/Middle_Langevin_MD.cu -rdc=true -lcudadevrt -lcuda -lcudart -lcufft -lnvrtc --use_fast_math -O4 -ldl -std=c++11 -arch=sm_50 -DCUDA_ARCH_BIN=50nvcc -o thermostats/Andersen_thermostat.o -c thermostats/Andersen_thermostat.cu -rdc=true -lcudadevrt -lcuda -lcudart -lcufft -lnvrtc --use_fast_math -O4 -ldl -std=c++11 -arch=sm_50 -DCUDA_ARCH_BIN=50nvcc -o thermostats/Berendsen_thermostat.o -c thermostats/Berendsen_thermostat.cu -rdc=true -lcudadevrt -lcuda -lcudart -lcufft -lnvrtc --use_fast_math -O4 -ldl -std=c++11 -arch=sm_50 -DCUDA_ARCH_BIN=50nvcc -o thermostats/nose_hoover_chain.o -c thermostats/nose_hoover_chain.cu -rdc=true -lcudadevrt -lcuda -lcudart -lcufft -lnvrtc --use_fast_math -O4 -ldl -std=c++11 -arch=sm_50 -DCUDA_ARCH_BIN=50nvcc -o barostats/MC_barostat.o -c barostats/MC_barostat.cu -rdc=true -lcudadevrt -lcuda -lcudart -lcufft -lnvrtc --use_fast_math -O4 -ldl -std=c++11 -arch=sm_50 -DCUDA_ARCH_BIN=50nvcc -o barostats/Berendsen_barostat.o -c barostats/Berendsen_barostat.cu -rdc=true -lcudadevrt -lcuda -lcudart -lcufft -lnvrtc --use_fast_math -O4 -ldl -std=c++11 -arch=sm_50 -DCUDA_ARCH_BIN=50nvcc -o barostats/andersen_barostat.o -c barostats/andersen_barostat.cu -rdc=true -lcudadevrt -lcuda -lcudart -lcufft -lnvrtc --use_fast_math -O4 -ldl -std=c++11 -arch=sm_50 -DCUDA_ARCH_BIN=50nvcc -o restrain/restrain.o -c restrain/restrain.cu -rdc=true -lcudadevrt -lcuda -lcudart -lcufft -lnvrtc --use_fast_math -O4 -ldl -std=c++11 -arch=sm_50 -DCUDA_ARCH_BIN=50nvcc -o constrain/constrain.o -c constrain/constrain.cu -rdc=true -lcudadevrt -lcuda -lcudart -lcufft -lnvrtc --use_fast_math -O4 -ldl -std=c++11 -arch=sm_50 -DCUDA_ARCH_BIN=50nvcc -o constrain/simple_constrain.o -c constrain/simple_constrain.cu -rdc=true -lcudadevrt -lcuda -lcudart -lcufft -lnvrtc --use_fast_math -O4 -ldl -std=c++11 -arch=sm_50 -DCUDA_ARCH_BIN=50nvcc -o constrain/SETTLE.o -c constrain/SETTLE.cu -rdc=true -lcudadevrt -lcuda -lcudart -lcufft -lnvrtc --use_fast_math -O4 -ldl -std=c++11 -arch=sm_50 -DCUDA_ARCH_BIN=50nvcc -o constrain/SHAKE.o -c constrain/SHAKE.cu -rdc=true -lcudadevrt -lcuda -lcudart -lcufft -lnvrtc --use_fast_math -O4 -ldl -std=c++11 -arch=sm_50 -DCUDA_ARCH_BIN=50nvcc -o virtual_atoms/virtual_atoms.o -c virtual_atoms/virtual_atoms.cu -rdc=true -lcudadevrt -lcuda -lcudart -lcufft -lnvrtc --use_fast_math -O4 -ldl -std=c++11 -arch=sm_50 -DCUDA_ARCH_BIN=50nvcc -o SITS/SITS.o -c SITS/SITS.cu -rdc=true -lcudadevrt -lcuda -lcudart -lcufft -lnvrtc --use_fast_math -O4 -ldl -std=c++11 -arch=sm_50 -DCUDA_ARCH_BIN=50nvcc -o collective_variable/collective_variable.o -c collective_variable/collective_variable.cu -rdc=true -lcudadevrt -lcuda -lcudart -lcufft -lnvrtc --use_fast_math -O4 -ldl -std=c++11 -arch=sm_50 -DCUDA_ARCH_BIN=50nvcc -o collective_variable/simple_cv.o -c collective_variable/simple_cv.cu -rdc=true -lcudadevrt -lcuda -lcudart -lcufft -lnvrtc --use_fast_math -O4 -ldl -std=c++11 -arch=sm_50 -DCUDA_ARCH_BIN=50nvcc -o collective_variable/RMSD.o -c collective_variable/RMSD.cu -rdc=true -lcudadevrt -lcuda -lcudart -lcufft -lnvrtc --use_fast_math -O4 -ldl -std=c++11 -arch=sm_50 -DCUDA_ARCH_BIN=50nvcc -o collective_variable/tabulated.o -c collective_variable/tabulated.cu -rdc=true -lcudadevrt -lcuda -lcudart -lcufft -lnvrtc --use_fast_math -O4 -ldl -std=c++11 -arch=sm_50 -DCUDA_ARCH_BIN=50nvcc -o collective_variable/combine.o -c collective_variable/combine.cu -rdc=true -lcudadevrt -lcuda -lcudart -lcufft -lnvrtc --use_fast_math -O4 -ldl -std=c++11 -arch=sm_50 -DCUDA_ARCH_BIN=50nvcc -o bias/restrain_cv.o -c bias/restrain_cv.cu -rdc=true -lcudadevrt -lcuda -lcudart -lcufft -lnvrtc --use_fast_math -O4 -ldl -std=c++11 -arch=sm_50 -DCUDA_ARCH_BIN=50nvcc -o bias/steer.o -c bias/steer.cu -rdc=true -lcudadevrt -lcuda -lcudart -lcufft -lnvrtc --use_fast_math -O4 -ldl -std=c++11 -arch=sm_50 -DCUDA_ARCH_BIN=50nvcc -o bias/Meta1D.o -c bias/Meta1D.cu -rdc=true -lcudadevrt -lcuda -lcudart -lcufft -lnvrtc --use_fast_math -O4 -ldl -std=c++11 -arch=sm_50 -DCUDA_ARCH_BIN=50nvcc -o wall/hard_wall.o -c wall/hard_wall.cu -rdc=true -lcudadevrt -lcuda -lcudart -lcufft -lnvrtc --use_fast_math -O4 -ldl -std=c++11 -arch=sm_50 -DCUDA_ARCH_BIN=50nvcc -o wall/soft_wall.o -c wall/soft_wall.cu -rdc=true -lcudadevrt -lcuda -lcudart -lcufft -lnvrtc --use_fast_math -O4 -ldl -std=c++11 -arch=sm_50 -DCUDA_ARCH_BIN=50nvcc -o plugin/plugin.o -c plugin/plugin.cu -rdc=true -lcudadevrt -lcuda -lcudart -lcufft -lnvrtc --use_fast_math -O4 -ldl -std=c++11 -arch=sm_50 -DCUDA_ARCH_BIN=50sed -i 's/\r//' mdin.txtsed -i 's/\r//' covid-tip4p/*nvcc -o SPONGEmain.o common.o control.o MD_core/MD_core.o bond/bond.o bond/bond_soft.o bond/listed_forces.o angle/angle.o angle/Urey_Bradley_force.o dihedral/dihedral.o dihedral/improper_dihedral.o cmap/cmap.o nb14/nb14.o neighbor_list/neighbor_list.o No_PBC/Coulomb_Force_No_PBC.o No_PBC/generalized_Born.o No_PBC/Lennard_Jones_force_No_PBC.o Lennard_Jones_force/Lennard_Jones_force.o Lennard_Jones_force/solvent_LJ.o Lennard_Jones_force/LJ_soft_core.o Lennard_Jones_force/pairwise_force.o PME_force/PME_force.o thermostats/Langevin_MD.o thermostats/Middle_Langevin_MD.o thermostats/Andersen_thermostat.o thermostats/Berendsen_thermostat.o thermostats/nose_hoover_chain.o barostats/MC_barostat.o barostats/Berendsen_barostat.o barostats/andersen_barostat.o restrain/restrain.o constrain/constrain.o constrain/simple_constrain.o constrain/SETTLE.o constrain/SHAKE.o virtual_atoms/virtual_atoms.o SITS/SITS.o collective_variable/collective_variable.o collective_variable/simple_cv.o collective_variable/RMSD.o collective_variable/tabulated.o collective_variable/combine.o bias/restrain_cv.o bias/steer.o bias/Meta1D.o wall/hard_wall.o wall/soft_wall.o plugin/plugin.o -rdc=true -lcudadevrt -lcuda -lcudart -lcufft -lnvrtc --use_fast_math -O4 -ldl -std=c++11 -arch=sm_50 -DCUDA_ARCH_BIN=50nvcc -o main_ti.o -c main_ti.cu -rdc=true -lcudadevrt -lcuda -lcudart -lcufft -lnvrtc --use_fast_math -O4 -ldl -std=c++11 -arch=sm_50 -DCUDA_ARCH_BIN=50nvcc -o PME_force/cross_PME.o -c PME_force/cross_PME.cu -rdc=true -lcudadevrt -lcuda -lcudart -lcufft -lnvrtc --use_fast_math -O4 -ldl -std=c++11 -arch=sm_50 -DCUDA_ARCH_BIN=50nvcc -o SPONGE_TImain_ti.o common.o control.o MD_core/MD_core.o neighbor_list/neighbor_list.o Lennard_Jones_force/LJ_soft_core.o PME_force/PME_force.o PME_force/cross_PME.o -rdc=true -lcudadevrt -lcuda -lcudart -lcufft -lnvrtc --use_fast_math -O4 -ldl -std=c++11 -arch=sm_50 -DCUDA_ARCH_BIN=50即可完成CudaSPONGE的编译构建，在当前路径下生成一个SPONGE可执行文件：
$ ll | grep SPONGE-rwxr-xr-x 1 root root 32455648 Nov 27 01:44 SPONGE*-rwxr-xr-x 1 root root7482232 Nov 27 01:44 SPONGE_TI*预处理
为了使得工作空间更加分明，这里我建议先创建一个独立的工作区：
$ mkdir work_dir准备一个待模拟的体系，例如我们这里使用一个简单的pdb纯蛋白体系：
REMARK Generated By Xponge (Molecule)ATOM 1 N ALA 1 -0.095 -11.436-0.780ATOM 2 CA ALA 1 -0.171 -10.015-0.507ATOM 3 CB ALA 1 1.201-9.359-0.628ATOM 4 C ALA 1 -1.107-9.319-1.485ATOM 5 O ALA 1 -1.682-9.960-2.362ATOM 6 N ARG 2 -1.303-8.037-1.397ATOM 7 CA ARG 2 -2.194-7.375-2.328ATOM 8 CB ARG 2 -3.606-7.943-2.235ATOM 9 CG ARG 2 -4.510-7.221-3.228ATOM 10 CD ARG 2 -5.923-7.789-3.136ATOM 11 NE ARG 2 -6.831-7.111-4.087ATOM 12 CZ ARG 2 -8.119-7.421-4.205ATOM 13NH1 ARG 2 -8.686-8.371-3.468ATOM 14NH2 ARG 2 -8.844-6.747-5.093ATOM 15 C ARG 2 -2.273-5.882-2.042ATOM 16 O ARG 2 -1.630-5.388-1.119ATOM 17 N ALA 3 -3.027-5.119-2.777ATOM 18 CA ALA 3 -3.103-3.697-2.505ATOM 19 CB ALA 3 -1.731-3.041-2.625ATOM 20 C ALA 3 -4.039-3.001-3.483ATOM 21 O ALA 3 -4.614-3.643-4.359ATOM 22 N ALA 4 -4.235-1.719-3.394ATOM 23 CA ALA 4 -5.126-1.057-4.325ATOM 24 CB ALA 4 -6.538-1.625-4.233ATOM 25 C ALA 4 -5.205 0.436-4.039ATOM 26 O ALA 4 -4.561 0.930-3.116ATOM 27OXT ALA 4 -5.915 1.166-4.728TER因为pdb格式经常会面临文件不完整的问题，所以需要使用Xponge进行预处理，安装方法如下：
$ python3 -m pip install xponge --upgrade文件处理的流程，这里用ipython的交互结果做一个简单的演示：
In : import XpongeIn : import Xponge.forcefield.amber.ff14sb # 导入力场Reference for ff14SB:James A. Maier, Carmenza Martinez, Koushik Kasavajhala, Lauren Wickstrom, Kevin E. Hauser, and Carlos Simmerling ff14SB: Improving the accuracy of protein side chain and backbone parameters from ff99SB Journal of Chemical Theory and Computation 2015 11 (8), 3696-3713 DOI: 10.1021/acs.jctc.5b00255In : C = Xponge.load_pdb("case1.pdb", ignore_hydrogen=False, ignore_unknown_name=True) # 加载pdb文件In : C.add_missing_atoms() # 补齐氢原子和其他丢失的residue atomIn : Xponge.save_pdb(C, "case1_fix.pdb") # 将新的体系保存到pdb文件中In : !mkdir proteinIn : Xponge.save_sponge_input(C, "protein/case1") # 保存SPONGE模拟所需参数文件Reference for Xponge:Xia, Y., Gao, Y. Q. Xponge: A Python package to perform pre- and post-processing of molecular simulations Journal of Open Source Software, 2022 7(77) 4467 DOI: 10.21105/joss.04467Out: Entity of Molecule: case1In : !ls -l protein/total 32-rwxr-xr-x 1 root root 1361 Nov 27 01:34 case1_LJ.txt-rwxr-xr-x 1 root root 2717 Nov 27 01:34 case1_angle.txt-rwxr-xr-x 1 root root185 Nov 27 01:34 case1_atom_name.txt-rwxr-xr-x 1 root root153 Nov 27 01:34 case1_atom_type_name.txt-rwxr-xr-x 1 root root 1437 Nov 27 01:34 case1_bond.txt-rwxr-xr-x 1 root root544 Nov 27 01:34 case1_charge.txt-rwxr-xr-x 1 root root 1639 Nov 27 01:34 case1_coordinate.txt-rwxr-xr-x 1 root root 4298 Nov 27 01:34 case1_dihedral.txt-rwxr-xr-x 1 root root977 Nov 27 01:34 case1_exclude.txt-rwxr-xr-x 1 root root371 Nov 27 01:34 case1_mass.txt-rwxr-xr-x 1 root root 3197 Nov 27 01:34 case1_nb14.txt-rwxr-xr-x 1 root root 16 Nov 27 01:34 case1_residue.txt-rwxr-xr-x 1 root root 20 Nov 27 01:34 case1_resname.txt这里除了补齐丢失的原子之外，还涉及到CudaSPONGE输入文件的问题，因此用Xponge来处理会相对便捷一些。到这里，就完成了CudaSPONGE分子模拟的预处理。
能量极小化
对于不同的模拟方法，我们需要给SPONGE输入不同的配置文件，例如能量最小化的一个配置文件的简单形式为minimize.txt：
case1 Minimizationmode = Minimization minimization_dynamic_dt 1default_in_file_prefix = protein/case1pbc=0 cutoff=999dt = 1e-02step_limit = 5000write_information_interval = 50rst = restartcoordinate_in_file =protein/case1_coordinate.txt在这个配置文件下，我们执行能量极小化的mode，参数文件保存在protein/目录下，并以case1开头。而模拟系统的笛卡尔坐标，由文件protein/case1_coordinate.txt给出。这个设置方便的地方在于，因为我们设置了restart参数，所以模拟结束之后会在当前路径下保存一个restart_coordinate.txt重启文件，所以下一次启动模拟的时候，只要把启动文件指向到这个restart坐标文件就可以了。配置好参数之后，运行的指令为：
$ ../SPONGE -mdin minimize.txt就可以获得相应的输出。
其他类型模拟
最常见的就是控温，那么主要就是设定mode=NVT，例如这是一个简单的nvt.txt，对应SPONGE的mdin输入文件：
case1 MD simulationmode = NVTdefault_in_file_prefix = protein/case1pbc=0 cutoff=999dt = 1e-3step_limit = 50000write_information_interval = 5000thermostat = middle_langevinmiddle_langevin_gamma = 10rst = nvt_restartcoordinate_in_file =restart_coordinate.txt这里起始坐标直接使用能量极小化之后的结果，并将NVT的最终坐标保存到nvt_restart_coordinate.txt文件中。其他如NPT模式的配置，可以参考这篇博客中的介绍。
增强采样
在CudaSPONGE v1.4的版本中，增强采样方法的定义形式如下meta.txt：
case1 MD simulationmode = NVTdefault_in_file_prefix = protein/case1pbc=0 cutoff=999dt = 1e-3step_limit = 50000write_information_interval = 5000target_temperature = 300.0thermostat = middle_langevinmiddle_langevin_gamma = 10rst = meta_restartcoordinate_in_file =nvt_restart_coordinate.txtcv_in_file = cv.txtdont_check_input = 1其中额外包含了一个CV的定义文件cv.txt，内容如下：
print{ CV = torsion}torsion{ CV_type = dihedral atom = 1 3 12 13}meta1d{ CV = torsion dCV = 0.06 CV_minimal = -3.1416 CV_maximum = 3.1416 CV_period = 6.2832 welltemp_factor = 50 height = 1 sigma = 0.3}一样的运行方法，可以看到输出结果如下：
$ ../SPONGE -mdin meta.txt SPONGE Version: v1.4 2024-01-01Sub-package: SPONGE, for normal molecular dynamics simulationsCitation: Huang, Y. - P., Xia, Y., Yang, L., Wei, J., Yang, Y.I.and Gao, Y.Q. (2022), SPONGE: A GPU - Accelerated Molecular Dynamics Package with Enhanced Sampling and AI - Driven Algorithms.Chin.J.Chem., 40 : 160 - 168. https ://doi.org/10.1002/cjoc.202100456MD TASK NAME: case1 MD simulationSTART INITIALIZING CONTROLLER Start initializing CUDA Compiled by CUDA 11.6 1 device found: Device 0: Name: NVIDIA GeForce RTX 3080 Ti Laptop GPU Memory: 16.0 GB Compute Capability: 86 Set Device 0 End initializing CUDA structure last modify date is 20231219END INITIALIZING CONTROLLERSTART INITIALIZING CV CONTROLLER: 1 CV defined 0 cv virtual atomsEND INITIALIZING CV CONTROLLERSTART INITIALIZING MD CORE: Mode set to NVT dt set to 0.001000 ps Start reading mass: End reading mass Start reading charge: End reading charge Start reading coordinate_in_file: atom_numbers is 57 system start_time is 50.000000 box_length is x: 999.000000 y: 999.000000 z: 999.000000 End reading coordinate_in_file Velocity is set to zero as default skin set to 2.00 Angstrom cutoff set to 999.00 Angstrom Start reading excluded list: excluded list total length is 290 End reading excluded list Start reading residue list: residue_numbers is 4 End reading residue list structure last modify date is 20211105END INITIALIZING MD CORESTART INITIALIZING MIDDLE LANGEVIN DYNAMICS: atom_numbers is 57 target temperature is 300.00 K friction coefficient is 10.00 ps^-1 random seed is 1476805525 structure last modify date is 20210826END INITIALIZING MIDDLE LANGEVIN DYNAMICSSTART INITIALIZING LENNADR JONES INFORMATION: atom_numbers is 57 atom_LJ_type_number is 8 structure last modify date is 20220601END INITIALIZING LENNADR JONES INFORMATIONSTART INITIALIZING COULOMB INFORMATION: structure last modify date is 20220603END INITIALIZING COULOMB INFORMATIONSTART INITIALIZING NB14 (nb14_in_file): non-bond 14 numbers is 135 structure last modify date is 20211222END INITIALIZING NB14LISTED FORCES IS NOT INITIALIZEDSTART INITIALIZING BOND (bond_in_file): bond_numbers is 56 structure last modify date is 20210830END INITIALIZING BONDSTART INITIALIZING BOND SOFT:END INITIALIZING SOFT BONDSTART INITIALIZING ANGLE (angle_in_file): angle_numbers is 99 structure last modify date is 20210830END INITIALIZING ANGLEUREY BRADLEY IS NOT INITIALIZEDSTART INITIALIZING DIHEDRAL (dihedral_in_file): dihedral_numbers is 137 structure last modify date is 20210830END INITIALIZING DIHEDRALIMPROPER DIHEDRAL IS NOT INITIALIZEDSTART INITIALIZING CMAP:CMAP IS NOT INITIALIZEDSTART INITIALIZING HARD WALL:END INITIALIZING HARD WALLSOFT WALLS ARE NOT INITIALIZEDRESTRAIN IS NOT INITIALIZEDSTART INITIALIZING RESTRAIN CV: 0 CV(s) found for restrainRESTRAIN CV IS NOT INITIALIZEDSTART INITIALIZING STEER CV: 0 CV(s) found for steerSTEER CV IS NOT INITIALIZEDSTART INITIALIZING META1D: 1 CV(s) found for meta1d CV 0: torsion reading 4 atom(s) for torsion atom 0: 1 atom 1: 3 atom 2: 12 atom 3: 13 type of 'torsion' is 'dihedral' reading 1 CV_period(s) for meta1d CV_period 0: 6.283200 reading 1 CV_minimal(s) for meta1d CV_minimal 0: -3.141600 reading 1 CV_maximum(s) for meta1d CV_maximum 0: 3.141600 reading 1 dCV(s) for meta1d dCV 0: 0.060000 reading 1 height(s) for meta1d height 0: 1.000000 reading 1 sigma(s) for meta1d sigma 0: 0.300000 reading 1 welltemp_factor(s) for meta1d welltemp_factor 0: 50.000000 Potential update interval is set to write_information_interval by default potential output file: meta1d_potential.txtEND INITIALIZING META1DVIRTUAL ATOM IS NOT INITIALIZEDSTART INITIALIZING CV PRINTER: 1 CV(s) found for print CV 0: torsion type of 'torsion' is 'dihedral'END INITIALIZING CV PRINTER------------------------------------------------------------------------------------------------------------ step = 5000, time = 55.000, temperature = 391.02, potential = -187.55, LJ = -6.25, Coulomb = -308.21, nb14_LJ = 7.49, nb14_EE = 23.77, bond = 19.29, angle = 31.16, dihedral = 43.88, meta1d = 1.32, torsion = -2.3809, ------------------------------------------------------------------------------------------------------------ step = 10000, time = 60.000, temperature = 298.28, potential = -183.35, LJ = -5.40, Coulomb = -316.07, nb14_LJ = 9.65, nb14_EE = 29.10, bond = 19.95, angle = 33.31, dihedral = 43.66, meta1d = 2.45, torsion = -2.5452, ------------------------------------------------------------------------------------------------------------ step = 15000, time = 65.000, temperature = 433.99, potential = -188.78, LJ = -4.70, Coulomb = -316.29, nb14_LJ = 8.71, nb14_EE = 23.72, bond = 21.29, angle = 26.82, dihedral = 47.90, meta1d = 3.77, torsion = -2.4958, ------------------------------------------------------------------------------------------------------------ step = 20000, time = 70.000, temperature = 249.71, potential = -183.19, LJ = -5.34, Coulomb = -329.13, nb14_LJ = 9.73, nb14_EE = 31.84, bond = 22.68, angle = 34.74, dihedral = 50.28, meta1d = 2.01, torsion = -1.9129, ------------------------------------------------------------------------------------------------------------ step = 25000, time = 75.000, temperature = 355.19, potential = -190.72, LJ = -7.80, Coulomb = -314.26, nb14_LJ = 8.21, nb14_EE = 23.10, bond = 19.06, angle = 29.59, dihedral = 48.39, meta1d = 3.01, torsion = -1.8429, ------------------------------------------------------------------------------------------------------------ step = 30000, time = 80.000, temperature = 407.06, potential = -181.22, LJ = 0.79, Coulomb = -293.82, nb14_LJ = 6.62, nb14_EE = 5.15, bond = 24.57, angle = 32.20, dihedral = 41.94, meta1d = 1.32, torsion = 0.4504, ------------------------------------------------------------------------------------------------------------ step = 35000, time = 85.000, temperature = 203.30, potential = -179.47, LJ = 0.97, Coulomb = -298.49, nb14_LJ = 8.28, nb14_EE = 4.97, bond = 27.75, angle = 39.17, dihedral = 35.27, meta1d = 2.61, torsion = 0.4398, ------------------------------------------------------------------------------------------------------------ step = 40000, time = 90.000, temperature = 310.20, potential = -190.12, LJ = -3.52, Coulomb = -296.07, nb14_LJ = 9.64, nb14_EE = 13.64, bond = 16.37, angle = 28.68, dihedral = 39.10, meta1d = 2.03, torsion = -0.0447, ------------------------------------------------------------------------------------------------------------ step = 45000, time = 95.000, temperature = 408.99, potential = -190.56, LJ = -2.71, Coulomb = -296.55, nb14_LJ = 8.19, nb14_EE = 10.34, bond = 19.28, angle = 30.85, dihedral = 36.49, meta1d = 3.57, torsion = 0.0334, ------------------------------------------------------------------------------------------------------------ step = 50000, time = 100.000, temperature = 462.33, potential = -189.09, LJ = -0.75, Coulomb = -293.79, nb14_LJ = 9.71, nb14_EE = 6.49, bond = 18.99, angle = 27.54, dihedral = 38.08, meta1d = 4.63, torsion = -0.0077, ------------------------------------------------------------------------------------------------------------Core Run Wall Time: 13.704983 secondsCore Run Speed: 315.220093 ns/dayEnd Pause总结概要
本文简单介绍了一下CudaSPONGE高性能分子动力学模拟软件，其基于原生的CUDA C开发，具有极高的模拟效率。结合前处理工具Xponge用于生成和处理输入文件，可以很好的兼容目前常用的很多力场形式。
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[*]https://www.cnblogs.com/bgalang/p/18316362
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