I think I've temporarily solved this problem. Only when I use
CUDA_VISIABLE_DEVICE to block the memory-almost-fully-occupied GPUs, I can run
GROMACS smoothly (using -gpu_id only is useless). I think there may be some bug
in GROMACS's GPU usage model in a multi-GPU environment (It seems like as
I also tried to restricting to different GPU using -gpu_id, but still with the
same error. I've also posting my question on
https://devtalk.nvidia.com/default/topic/1072038/cuda-programming-and-performance/cudafuncgetattributes-failed-out-of-memory/
Following is the output of nvidia-smi:
On 2/21/20 1:01 PM, Qing Liu wrote:
Dear Justin Lemkul,
Thanks for your reply. I just downloaded the Cryo-EM structure of the dimer
from RCSB, added missing residues using Modeller and built systems by the
following commands:
gmx pdb2gmx -f dimer.pdb -o dimer.gro -p
On 2/22/20 9:41 AM, Neena Susan Eappen wrote:
Thank you Justin, just sharing the sample script here:
#!/bin/bash
for i in {1..n}
do j=$((i+1))
gmx grompp -f nvt.mdp -c em${i}.gro -r em${i}.gro -p topol.top -o nvt${j}.tpr
gmx mdrun -deffnm nvt${j}
gmx grompp -f md.mdp -c
Thank you Miro, but I don't think I found what I wanted in your script. Let me
be more clear: I ran n simulations in a loop, I have corresponding n energy
files (.edr). I want to extract potential energy from each file. How would I go
about that with a script?
Many thanks,
Neena
I have something like this on my github.
https://github.com/Miro-Astore/gromacs_scripts/tree/master/pbs_files/gadi
File is memb0.pbs let me know if you have any questions.
On Sat., 15 Feb. 2020, 8:45 am Neena Susan Eappen, <
neena.susaneap...@mail.utoronto.ca> wrote:
> Hello gromacs users,
>
>
Thank you Justin, just sharing the sample script here:
#!/bin/bash
for i in {1..n}
do j=$((i+1))
gmx grompp -f nvt.mdp -c em${i}.gro -r em${i}.gro -p topol.top -o nvt${j}.tpr
gmx mdrun -deffnm nvt${j}
gmx grompp -f md.mdp -c nvt${j}.gro -t nvt${j}.cpt -p topol.top -o
Thank you Mark! Sorry could you please explain the details of "stdin" of
"pdb2gmx"? Is there a link for it?
I think "echo" only works for choosing the force field, but not work for the
charge assignment.
e.g. when I use:
echo 15 0 0 0 0 | gmx pdb2gmx -f protein.pdb -o protein_processed.gro
Hi,
Echo works just fine - you just need a way to script what input it injects
to the stdin of pdb2gmx. That's logic you need for any solution so is
probably easiest. The expect tool may be another option.
Mark
On Fri., 21 Feb. 2020, 21:41 ZHANG Cheng, <272699...@qq.com> wrote:
> I want to run
