nohup gmx mdrun -pin on -deffnmHPEP_WTfx1_gpumd-v & 现在可以成功跑，但是无法调用GPU，跑100ns...
超算上装的gromacs（2018.8），能调用gpu nvt.mdp如下 nvt.mdp(2.63 KB, 下载次数 Times of ...
选择新生成的蛋白配体复合物 gmx trjconv -f md.xtc -s md.tpr -n prolig.ndx -o prolig.xtc # 生成只包含复合物的tpr文件,选择复合物组 gmx convert-tpr -s md.tpr -n prolig.ndx -o prolig.tpr # 利用新的tpr文件rerun新的xtc文件,生成edr gmx mdrun -s prolig.tpr -rerun prolig.xtc -e...
MdRunSubscription].745 ###746747 # We are giving the director a resource that contains the subscription748 # to the dispatched work.749 for member in range(self.ensemble_width):File ~/mambaforge/envs/dmref/lib/python3.10/site-packages/gmxapi/simulation/mdrun.py:390, in LegacyImplementation...
under certain occasions system Boost can be picked up with higher priority than the bundled one. For some reason, this seems to affect only builds where GPU support with OpenCL is enabled (-DGMX_GPU=OpenCL). (I don't have a machine at hand to test if it also affects CUDA/SYCL the ...
Re: [gmx-users] Optimising mdrun Kevin Boyd Re: [gmx-users] Optimising mdrun Robert Cordina [gmx-users] 1 particles communicated to PME rank 3 are more than 2/3 times the cut-off out Seketoulie Keretsu Re: [gmx-users] 1 particles communicated to PME rank 3 are more than 2/3 ti...
Re: [gmx-users] Gromacs: GPU detection Szilárd Páll [gmx-users] Re: Gromacs: GPU detection Brad Van Oosten Re: [gmx-users] Re: Gromacs: GPU detection Szilárd Páll Re: [gmx-users] Re: Gromacs: GPU detection Szilárd Páll [gmx-users] Trying to explain differences in behaviour bet...
本人的服务器上有100块CPU，5块GPU, 做MD的时候使用命令 gmx mdrun -v -deffnm simulation 发现GPU...
以下是gmx_mpi mdrun -h的部分输出：OPTIONS Options to specify input and output files:-s [<....
>> GPU support: enabled >> disabled >> invsqrt routine: gmx_software_invsqrt(x) >> same >> CPU acceleration: SSE4.1 >> AVX_256 >> FFT library: fftw-3.2.2 >> >> fftw-3.3.3-sse2 >> Large file support: enabled >> same