[gmx-users] About extend the run,,
Justin A. Lemkul
jalemkul at vt.edu
Sat Jun 2 16:42:02 CEST 2012
On 6/2/12 10:27 AM, rama david wrote:
> Hi Gromacs Friends,
> I run a Production run with saving the co-ordinates and velocity
> after every 500 steps for 20ns..
> Now I want to extend the run but with saving the co-ordinates and velocity
> after every 1000 steps for next 30ns (total 50ns)
> To perform these task I am using following command
> 1. grompp -f <New mdp file just change in saving output> -t <.cpt> -c <.gro
> file(gro file from position restrained run )> -o new.tpr
> 2. tpbconv -s new.tpr -0 extend.tpr -extend 30000
> 3. mdrun -v -deffnm extend -cpi <.cpt> -append
> Is these approach is correct??
No. The new.tpr file contains instructions to run from 20 -> 30 ns. There is
no need to then invoke tpbconv. You would also need a new invocation of mdrun,
since the output frequencies won't match. You don't want to append those files
with mdrun (nor will the checkpoint file likely let you).
> Second query;
> To rerun the crash run, users give .cpt file as input to -mdrun,
> My query is, There are two cpt file a) pre.cpt b) .cpt ,
> So which one has to given as input???
Use gmxcheck to understand the contents of each. The timestamp will also tell
you a difference, as will reading mdrun -h for an explanation of what the -cpt
option is doing.
Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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