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mpiexec gmx_mpi_d mdrun Note that '_mpi' indicates a parallel executable and '_d' indicates a program built with double precision ('_gpu' denotes a GPU executable built with CUDA). See the module help output for specific versions for more details on executable naming conventions.

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#!/bin/bash yhrun -N 1 -n 1 -p debugg gmx_mpi grompp -f rf_verlet.mdp yhrun -N 2 -n 24 -p debug gmx_mpi mdrun -ntomp 1 说明： 1）参数“-ntomp 1”设置每个mpi进程开启1个线程。 8.5 提交脚本. yhbatch -N 2 -n 24 -p debug sub.sh . 8.6 测试结果. 计算结束后，可以在结果文件中查看计算结果。

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thread-MPI threads: MPI-based threading model implemented as part of GROMACS, incompatible with When running on 1 or more GPUs, by default GROMACS will: detect the number of available...

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以下是gmx_mpi mdrun -h的部分输出： ... pinning threads from different mdrun instances to the same core-pinstride <int> (0) Pinning distance in logical cores ...

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书接上回。 Supernova：使用Gromacs 5.1.5进行REMD模拟由于Gromacs 5在我的机器上运算速度不佳，研究了使用新版Gromacs进行REMD模拟的方法，以便尽可能高效地利用计算资源。 本文所用方法为基于上文改动而成。 0. …

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esculentin-1a 201 1gly n 1 0.133 0.000 0.000 1gly h1 2 0.118 -0.094 0.030 1gly h2 3 0.185 0.049 0.070 1gly h3 4 0.045 0.045 -0.014 1gly ca 5 0.207 0.000 -0.125 1gly c 6 0.234 0.140 -0.176 1gly o 7 0.196 0.174 -0.288 2ile n 8 0.300 0.221 -0.094 2ile h 9 0.328 0.188 -0.004 2ile ca 10 0.332 0.359 -0.132 (...) 21gly c 199 -1.436 0.231 -2.356 21gly o1 200 -1.539 0.169 -2.328 21gly o2 201 -1.386 0 ... 在第三章, 我们解释了如何在mdrun中使用 原子组 (参看3.3节). 对大多数分析程序, 你也必须选择原子组. 虽然大多数程序都能产生一些默认的索引组, 但这些程序总是可以从索引文件中读入组. 让我们考虑一个具体的例子, A和B双组分混合物的模拟.

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