[gmx-users] part number in extending simulation

Dommert Florian dommert at icp.uni-stuttgart.de
Sun Aug 28 12:53:59 CEST 2011

On Sun, 2011-08-28 at 17:55 +0800, Hsin-Lin Chiang wrote: 
> Hi Flo,
> Thank you for reply.
> I got it.
> But as you see I also indicate the new names for output files.
> Do I get correct result in this kind of situation?
> Or I need to rerun it with "-noappend"

I am not sure, but I assume if you set new names, new files will be
created. The checkpoint input files contains important information about
your coordinates, velocities, states of random number generators for the
NH coupling .... That is the reason, why it is necessary for a
continuous extension of your run. The results should not depend on the
append option, only the number of resulting trajectories is affected.
The suffix "part???" will just arise if the files are already present
and you use -noappend. Now you will end up with two trajectories I

* md50ns,
* md100ns,

which are indistinguishable from a single continuous 100ns run and I
think that is what you want, isn't it ?


> Sincerely yours,
> Hsin-Lin
> >Hi,
> >
> >check the standard options of mdrun with the help flag -h of version
> >4.5.4 and below. You will realize, that the standard append behaviour
> >changed from "no" to "yes". Hence if you start from a checkpoint and
> >files are already present in the working directory the integration
> >results will be appended.
> >
> >Flo

Florian Dommert
Dipl. - Phys.

Institute for Computational Physics
University Stuttgart

Pfaffenwaldring 27
70569 Stuttgart

EMail: dommert at icp.uni-stuttgart.de
Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert

Tel.: +49 - (0)711 - 68563613
Fax.: +49 - (0)711 - 68563658
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