Re: [gmx-users] Regarding extending simulations with change in .mdp file

Hi, gmx grompp -f first -o first gmx mdrun -deffnm first gmx grompp -f second -o second gmx mdrun -deffnm second -cpi first does what I think you should want. You end up with output files named first.* and second.* which you can concatenate with trjconv or eneconv if what you plan to do with them

[gmx-users] Regarding extending simulations with change in .mdp file

Hello, I have ran a energy minimization, followed by nvt, followed by md run. My md run mdp (ie., md.mdp) has dt = 0.002, nsteps = 3000 ; [0.002 * 3000 = 6 ps (60 ns)] nstxout = 5000 ; save coordinates every 10.0 ps nstvout = 5000 ; save velocities every 10.0 ps nstenergy = 5000 ; sav

Re: [gmx-users] Regarding extending simulations

and which are the commands tht i need to give there.. gmx trjconv or gmx grommp ..?? Can anybody guide me through this kindly.. Sent with Mailtrack On Sun, May 21,

[gmx-users] Regarding extending simulations

Hello, I have ran a energy minimization, followed by nvt, followed by md run. My md run mdp (ie., md.mdp) has dt = 0.002, nsteps = 3000 ; [0.002 * 3000 = 6 ps (60 ns)] nstxout = 5000 ; save coordinates every 10.0 ps nstvout = 5000 ; save velocities every 10.0 ps nstenergy = 5000 ; save

Re: [gmx-users] Regarding extending simulations

Hi, Your first run used gmx mdrun -deffnm, and like the error message says, the checkpoint file knows what the output filenames were in that case. But your second mdrun doesn't specify -deffnm, so mdrun doesn't know whether you meant to append to the old files, or not provide that checkpoint file,

[gmx-users] Regarding extending simulations

Hello, I ran a md run of 20ns [1000*.002] and i got the files as md.edr, md.log, md.tpr, md.gro, md.xtc, md.cpt etc., Now i want to extend/continue my simulation from 20 ns to again 20 ns (total 40 ns). So i gave the command as - gmx convert-tpr -s md.tpr - extend 2 -o md1.tpr gmx mdrun -v