Hi M. Khattab,

Any file with an extension .sh is a shell script file. I am attaching an example file below.

gmx grompp -f nvt.mdp -c em.pdb -p topol.top -n index.ndx -o nvt.tpr

gmx mdrun -v -s nvt.tpr -c nvt.pdb

gmx grompp -f npt.mdp -c nvt.pdb -p topol.top -n index.ndx -t state.cpt -o npt.tpr

gmx mdrun -v -s npt.tpr -c npt.pdb

gmx grompp -f md.mdp -c npt.pdb -p topol.top -n index.ndx -t state.cpt -o md.tpr

gmx mdrun -v -s md.tpr -c md.pdb

just copy the content to a text editor and save file as "run.sh" or any name you wish.

To run this file just make the file executable and run using "./name of file.sh", of course in that particular folder.

Before you submit .sh file to supercomputer perform all the necessary previous steps including pdb2gmx, ediconf, solvation, ions addition, minimization. because after these steps NVT, NPT equilibration and MD run commands can run in sequence. You don't have to manually add parameters or any values.

Also it is not necessary to to convert .pdb file to .gro format as gromacs can read and write .pdb files, you just have to specify it by command -c name_of_file.pdb

regards

Tanuj Sharma

It is the same as submitting the jobs on a local machine assuming that gromacs is installed on the server. You need exactly the same files and the command sequence is exactly the same. After logging into the server, you shall probably need to ssh to a compute node and then cd to the directory where the pdb file is located (or create a directory with mkdir and scp the pdb file there). Now, as for preparing the protein and the system, I would suggest you to follow the excellent tutorial by Dr. Lemkul (http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/index.html).

All the .tpr, .top, .cpt etc. files shall be created by gromacs commands. However, you shall need three .mdp files. The tutorial I suggested above shall also provide you those three .mdp files. 

Finally, in order to utilize the full potential of the supercomputer, you need to assign the number of CPUs for the mdrum job. So, the last command, as suggested by Tanuj Sharma, needs an additional flag -np X, where X is the number of processors, which can be the maximum number of processor available at that compute node.

Thanks all !

When i was using Gaussian on supercomputer, I had to prepare script and input files. Script file contains

#!/bin/bash

#PBS -l walltime=39:00:00

#PBS -l nodes=1:ppn=8

#PBS -l mem=30GB

#PBS -q sstar

#PBS -N AG

source /usr/local/modules/init/bash

module load gaussian

cd $PBS_O_WORKDIR

g09 5.out 2>&1

While input file contains the following + molecular coordinates

%nprocshared=8

%chk=AG.chk

%mem=20GB

# opt freq B3LYP/6-311+G* geom=connectivity gfinput

opt

So my question is, shall i do the same with gromacs (prepare script and input files) ??!!! 

The command should be written in input file or in ssh window?!

Hi Muhammad,

Are you using supercomputing facility from NCI. If you do you can use their guide and get along on your way. If you still face any issues just drop me a message and I will be happy to help you.

Hi Vishal,

No, I am using Swinburne supercomputing facility. Unfortunately, I have no experience with programming and computer languages.

Regarding the queue submission your computer administrator can help. You might as well need to load gromacs module in your local environment. However, the initial pre-processing steps are interactive. For example, while running pdb2gmx you shall be asked to select a force field; while adding ions you shall be asked to to select which molecules to replace. So, you actually need to pass those commands one by one in the ssh window (alternatively, you can do the pre-prossessing in your local computer then transfer the files to the server). The final six commands (as mentioned by Tanuj Sharma) can be put into a script and submitted to the queue. The queue submission or batch submission processes differs in different clusters. In our server, we use qlogin to log into a free node (or check the node status using qstat -f and then ssh to a free node) and then run the commands as we do in the local computer. However, it is not the optimal use of resources. You should use the qsub as you do with gaussian.

I have been in trouble to figure out how to load executable GROMACS file. Could you help with how to load GROMACS? then I can start with pdb2gmx command?

Is it not already in the path? Have you tried gmx? Check what is written on those GMXRC files. vi GMXRC.bash. Most probably, environment variables are defined there. If so, you can try ./GMXRC.bash in a bash shell or ./GMXRC.csh in a c shell. Or try source GMXRC in a bash shell. Then try gmx.

All didn't work except GMXRC. It gave me the following

/usr/local/x86_64/gnu/gromacs-5.0.5/bin/GMXRC: line 14: return: can only `return' from a function or sourced script

/usr/local/x86_64/gnu/gromacs-5.0.5/bin/GMXRC: line 17: CSH:: command not found

/usr/local/x86_64/gnu/gromacs-5.0.5/bin/GMXRC.csh: line 8: syntax error near unexpected token `setenv'

/usr/local/x86_64/gnu/gromacs-5.0.5/bin/GMXRC.csh: line 8: `if (! $?LD_LIBRARY_PATH) setenv LD_LIBRARY_PATH ""'

If applicable, my skype ID is [email protected]. If you added me, I can share screen with you and get a real-time advises to load gromacs.

Thanks in advance,

Muhammad 

Try these commands one by one:

exec bash

source /usr/local/x86_64/gnu/gromacs-5.0.5/bin/GMXRC.bash

gmx

Didn't work too. 

Another question, how to check if gromacs is loaded or not? is it by "gmx -version"?

It also tell me command not found.

Hi Muhammad

try writing

source /usr/local/x86_64/gnu/gromacs-5.0.5/bin/GMXRC

then type command

gmx pdb2gmx -h

to check version. the command also can be used to convert pdb files to gromacs readable format.

regards

Tanuj

Thanks all for your kind assistance!