[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.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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