GROMACS version:2020.3
GROMACS modification: Yes/No
In order to extend (or reinitiate) an MD simulation (say from 25 ns to 100ns), one of the options in gromax is to use the ‘-extend’ option as in gmx convert-tpr, wherein, the velocities are coordinates are retrieved from the earlier .trr (trajectory) and the energy (.edr) files.
The following script used to run for an earlier version of GROMACS (in my collaborator’s system) with -f for the existing trajectory and -e for the energy input files.
Production
set cnt = 1
set cntmax = 10
while ( {cnt} <= {cntmax} )
if ( {cnt} == 1 ) then
gmx grompp -f step5_production.mdp -o step5_{cnt}.tpr -c step4.1_equilibration.gro -n index.ndx -p topol.top
gmx mdrun -v -deffnm step5_{cnt}
else
@ pcnt = {cnt} - 1
gmx convert-tpr -s step5_{pcnt}.tpr -f step5_{pcnt}.trr -e step5_{pcnt}.edr -o step5_{cnt}.tpr -extend 1000
gmx mdrun -v -deffnm step5_${cnt}
endif
@ cnt += 1
end
However, in the current version (version 2020.3) of gromacs that I am using in my server, the -e and -f options seem to be valid no more.
Command line:
gmx convert-tpr -s 6vw1_AE-orig_md_25ns.tpr -f 6vw1_AE-orig_md_25ns.trr -e 6vw1_AE-orig_md_25ns.edr -o 6vw1_AE-orig_md_100ns.tpr -extend 75000
Program: gmx convert-tpr, version 2020.3
Source file: src/gromacs/commandline/cmdlineparser.cpp (line 275)
Function: void gmx::CommandLineParser::parse(int*, char**)
Error in user input:
Invalid command-line options
Unknown command-line option -f
Unknown command-line option -e
The command however runs fine without returning an error in a reduced form.
gmx convert-tpr -s 6vw1_AE-orig_md_25ns.tpr -o 6vw1_AE-orig_md_100ns.tpr -extend 75000
We are not sure opting this would be correct as we are unsure of how the latest velocities (or for that matter coordinates) are passed on to the next MD run without the .trr and .edr inputs.
Any help would be deeply appreciated.