[gmx-users] continuing the terminated simulation

[Pavan Ghatty]

mdrun -deffnm md_0_1
If the above crashed, do the following:
mdrun -s md_0_1.tpr -cpi md_0_1.cpt -deffnm md_0_2
This way, pre-crash files are called md_0_1 and post-crash file will be
named md_0_2[.cpt.gro.xtc.trr...]. The simulation will end when it reaches
the number of steps entered in the initial .tpr file which is md_0_1.tpr in
your case.

hth
Pavan


On Wed, Oct 30, 2013 at 5:36 AM, Ankita Naithani
<ankitanaithani at gmail.com>wrote:

> Hi Delara,
>
> To continue a crashed simulation you just need to type in the following
> command without deffnm md.
>
> mdrun -s md_0_1.tpr -cpi md_0_1.cpt
>
> You can check the link here:
> http://www.gromacs.org/Documentation/How-tos/Doing_Restarts
>
> The continuation is down via the .cpt file. the _prev.cpt is just a backup
> copy and you need only .cpt file to begin the crashed run.
> The difference is explained here:
> http://www.gromacs.org/Documentation/File_Formats/Checkpoint_File
>
> Cheers,
>
> Ankita
>
>
>
>
> On Wed, Oct 30, 2013 at 9:26 AM, delara aghaie <d_aghaie at yahoo.com> wrote:
>
> > Dear Gromacs users
> > Hello,
> > I use gromacs version 4.5.5. I have started with Lysozime in water
> > simulation. (Justin tutorials)
> > The md part of simulation was terminated. Now I want to continue the
> > simulation from the interruption point. Is this command line correct?
> > mdrun -deffnm md_0_1      -s    md_0_1.tpr       -cpi
> > md_0_1.tpr.cpt???
> >
> > I am not sure whether to use only -cpi md_0_1.tpr.cpt with mdrun command
> > or both .tpr and .cpt files???
> >
> > another question is that whether continuing the simulation should be done
> > via file md_0_1.tpr.cpt  or md_0_1.tpr_prev.cpt ? and what in the
> > difference between them?
> >
> > Thanks in advance
> > Regards
> > D.M
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>
> --
> Ankita Naithani
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