this to me seems like an issue with your script, which this isn’t the forum for.
Nevertheless, my guess is that the count variable is not being updated in the loop (since all your modifications are in nvt_0.mdp). How to solve that depends on which type of script or shell you are using. For example, in bash incrementing is not as easy as doing count++.
thanks for replying
does the command “gmx grompp -f nvt_$count.mdp -p topol.top -c em.gro -o nvt_$count.tpr;”
creates file called nvt_.mpd for each time ? i mean if the codes runs successfully. is that okay ? i searched for site or link illustrate which this options ( -f , -p ,-o) indicates ! but couldn’t find
Sorry, what do you mean? grompp will not create nvt_.mdp unless you specifically use the -po flag. If the command completes successfully it managed to read the input from -f, if it fails you will see that in the standard error terminal output.
If grompp sets ref-t = 0 it means such a line is in the .mdp file. If that is not what you expect, please ensure that your script is doing what you think it does. I cannot give specific advice for that.
The script you showed above has a number of syntax problems and doesn’t use values for temperature like what you’re showing here, so I can’t comment on what’s going on for sure, but if your .log file says the ref-t value was set to 0 K, then your simulation will do a whole lot of nothing. No atoms should move at that temperature, by definition. You need to revisit how you’re generating your .mdp files and verifying their contents before running the simulations.