for i in 1 2 3 4 5 6 7 8 9 10 ;do
gmx grompp -f nvt$i.mdp -p topol.top -c em.gro -o tprout.tpr
mpirun -np 10 gmx_mpi mdrun -multidir sim1 sim2 sim3 sim4 sim5 sim6 sim7 sim8 sim9 sim10 -deffnm tprout -replex 500
File input/output error:
Your for-loop is not being performed in any kind of subdirectory, so you’re regenerating a file with the same name each time. Then
mdrun complains that the input file isn’t in the relevant directories. You need to generate a
.tpr file in each subdirectory, not in some top-level directory (which is going to be continually over-written as you have it constructed).
Thanks a lot for replying excuse me I searching for solving this problem but couldn’t generate the tpr in the sub-directory and you help, please?
i tried also to implement this command in each directory manually
gmx grompp -f nvt1.mdp -c em.gro -p topol.top -o tprout.tpr
but didn’t get the tpr output and got this warning
Program: gmx grompp, version 2018.1
Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 2406)
Too many warnings (1).
If you are sure all warnings are harmless, use the -maxwarn option.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
i think that becasue the different veriosn of gromacs as i installed 2020.4 but got with this warning ```
gmx grompp, version 2018.1
how can i remove this version 2018.1 , please ?
You need to descend into each subdirectory within the for-loop, then return to the top-level directory after the
grompp command is complete.
If you’re getting warnings, you need to inspect where they’re coming from. You haven’t posted what the warning actually is, so no one can possibly help you sort it out.
No idea. How and where did you install it? Where is the 2020.4 version installed? How did you configure your environment? If you want to have multiple versions installed and selectively use one version or another, you need to have good organization of your files and environment.
The warning tells you what to do. Your
tau-p value is too small in light of the other settings being applied.
i set it to be 0.2 should increase it ?
You set it to 0.5 according to the warning. And given that the value of
nstpcouple*dt is 0.12,
tau-p must be at least 10x larger. So 1.2 is the minimum value to set for
tau-p. The value of
nstpcouple*dt is a little oddly large, because normally one uses a
tau-p value on the order of 0.5 - 1.0 with the Berendsen barostat.