[gmx-users] extending simulation without cpt file

[Yongchul Chung]

Thanks Justin! it works now.

Greg

On Wed, Nov 3, 2010 at 7:39 PM, Mark Abraham <mark.abraham at anu.edu.au>wrote:

> ----- Original Message -----
> From: Mark Abraham <mark.abraham at anu.edu.au>
> Date: Thursday, November 4, 2010 10:38
> Subject: Re: [gmx-users] extending simulation without cpt file
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>
> >
> >
> > ----- Original Message -----
> > From: Yongchul Chung <yxc169 at case.edu>
> > Date: Thursday, November 4, 2010 10:28
> > Subject: [gmx-users] extending simulation without cpt file
> > To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> >
> > > Hello gmxers,
> > >
> > > I am using GROMACS 4.0.3. I have original trr, edr, log and tpr file
> but erased cpt file. However, I need to extend the simulation from the end
> of the trajectory file. I know this will not be binary identical as stated
> here (http://www.gromacs.org/Documentation/How-tos/Extending_Simulations).
> I used following commands.
> > >
> > > tpbconv -s topol.tpr -extend 102000 -o topolnew.tpr
> > > mdrun -s topolnew.tpr
> > >
> > > When I do this and run the simulation, for some reason, the simulation
> starts from t=0 instead of t=102000. it seems like gromacs is writing the
> file without recognizing it that it should start the trajectory from 102000
> ps. Is this a known bug? If so, is there a way around to solve this problem?
> >
> > You've extended the run time of the original simulation, and forced it
> to start from the state in the new .tpr, but that state came from the
> original .tpr. By contrast, mdrun -s -cpi replaces the .tpr state with that
> of the checkpoint.
> >
> > Your best chance of continuing will come from reconstructing the .mdp
> suitably (use gmxcheck to compare resulting .tpr files) and using grompp to
> create a .tpr using the most recent endpoint permitted by your .trr + .edr.
>
> Actually, Justin's right. tpbconv needs -e -t files. It's been so long
> since I used it, I'd forgotten :-)
>
> Mark
>
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