Unable to run REMD simulation

User discussions
1

GROMACS version: 2019.5
GROMACS modification: No

Dear users,

I am trying to run a REMD simulation, with the replica files in the working directory having names like testrun_1.tpr, testrun_2.tpr, etc.

However, upon running the command below with SLURM architecture:

mpirun gmx_mpi mdrun -s testrun_.tpr -v -deffnm testrun_ -replex 500 >> replex_1.log

I get errors like:

Error in user input:
Invalid command-line options
In command-line option -s
File ‘testrun_.tpr’ (or ‘testrun_’) does not exist or is not accessible.
The file could not be opened.
Reason: No such file or directory
(call to fopen() returned error code 2)

Even the ‘-multi’ option is not being recognized:

Error in user input:
Invalid command-line options
In command-line option -s
File ‘testrun_.tpr’ does not exist or is not accessible.
The following extensions were tried to complete the file name:
.tpr
Unknown command-line option -multi

Please advise on how to proceed further regarding this. Thanks a lot.

2

Quick question,

Have you tried placing all of the different tpr’s in different directories and used -multidir? I know in 2020 -multi was removed and you need to use -multidir instead

3

Hi Mick,

Unfortunately the tutorials (or notes?) available were not very clear, so had to devise something on my own which indeed involved the “-multidir” flag. The command below worked finally:

mpirun gmx_mpi mdrun -v -deffnm testrun -multidir {1…68} -replex 500 >> replex.log

Although I have another question, is it recommended to use the “-multidir” flag for the “grompp” and the typical “mdrun” commands too? Of course, the “-replex” flag will not be present then. Please let me know your thoughts regarding this.

Cheers
Peter

4

excuse me did you use for loop for this command ?

5

No, I executed the command as above.