I want to extend my simulation. I use Gromacs 2018.4. At the beginning (20ns) I use Berendsen thermostat and barostat and then (80ns) I change mdp file and use Nose-Hoover thermostat and PArinello-rahman barostat.
So I want to extend my simulation with changing mdp files. (I also change things like continution yes, gen-vel=no etc.)
So I wrote this:
gmx grompp -f eq1_dgdg295.mdp -c em.gro -r em.gro -p system.top -o eq1
then
gmx mdrun -deffnm eq1 -cpi checkpoint1.cpt
But after that I cant find my checkpoint1.cpt file! I dont know why!
After this I try to extend my simulation:
gmx grompp -f eq2_dgdg295.mdp -c checkpoint1.cpt -p system.top -o eq2
But I have this error:
Error in user input:
Invalid command-line options
In command-line option -c
File name 'checkpoint1.cpt' cannot be used for this option.
Only the following extensions are possible:
.gro, .g96, .pdb, .brk, .ent, .esp, .tpr
I used this instructions:
To use the checkpoint file for a restart, use a command line such as
gmx mdrun -cpi state
Changing mdp options for a restart
If you wish to make changes to your simulations settings other than length, then you should do so in the mdp file or topology, and then call
gmx grompp -f possibly-changed.mdp -p possibly-changed.top -c state.cpt -o new.tpr gmx mdrun -s new.tpr -cpi state.cpt
to instruct gmx grompp to copy the full-precision coordinates in the checkpoint file into the new tpr file. You should consider your choices for tinit, init-step, nsteps and simulation-part. You should generally not regenerate velocities with gen-vel, and generally select continuation so that constraints are not re-applied before the first integration step.
http://manual.gromacs.org/documentation/2018.4/user-guide/managing-simulations.html
The -c flag in gmx grompp calls for a structure file (*.pdb, *.gro). For instance, you could pass it the last frame of your 20 ns trajectory.
If you want to use gmx grompp with a checkpoint file, you can also use the optional -t flag.
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