[gmx-users] About gromacs run...

Mark Abraham Mark.Abraham at anu.edu.au
Sat Jan 2 15:05:12 CET 2010

Henry Yang wrote:
> Dear users,
> Happy new yera to all.
> I have just a very simple query..
> I am running a simulation for 100 ns. I have decided to run it by 10 ns 
> step of each. In every run, the gromacs generated confout.gro file, the 
> traj.trr, traj.xtc, md.log , ener.edr file, state.cpt etc. The next time 
> when i run the simulation for the next 10 ns , I have edited the em.mdp 

It's probably best not to name your simulation .mdp file "em.mdp" which 
would normally be for an Energy Minimization.

> file and just change the tinit to the last time that i was run and the 
> nsteps to 5000000 for 10 ns.. And the command i used for grompp is ...
> grompp -f em.mdp -c confout.gro -p topol.top -o topol.tpr 
> And then it will generate the topol.tpr file. and the command is then
> mdrun
> My question is is that oaky ... or I have to use any more file in the 
> grompp command like that traj.trr or state.cpt for tracking velocity??

With the advent of checkpointing in GROMACS 4, there's no reason to want 
to use this strategy. Consult the GROMACS wiki pages on restarts and 
continuing runs. Set up your original grompp for your expected maximum 
run, and choose an appropriately conservative checkpoint interval in the 
mdrun command line, and suitable n*out .mdp options. If later you need 
to extend the run, use tpbconv -extend and supply the final checkpoint 
file to the next mdrun. There should be no need in 4.x to re-use grompp 
unless you need to change something more than the length of the simulation.


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