[gmx-developers] RE: gmx-developers Digest, Vol 96, Issue 13

[Dmitry Nerukh]

Thanks, Mark.  Can you give me a hint in what function is the best to look
for the code?

As for nstxtcout, etc I understand that it only outputs in xtc format, that
is only coordinates?  But I need velocities as well.

Dmitry.

> Message: 5
> Date: Wed, 11 Apr 2012 10:24:38 +1000
> From: Mark Abraham <Mark.Abraham at anu.edu.au>
> Subject: Re: [gmx-developers] local atom number from global atom
> 	number
> To: Discussion list for GROMACS development
> 	<gmx-developers at gromacs.org>
> Message-ID: <4F84CF46.4010200 at anu.edu.au>
> Content-Type: text/plain; charset="iso-8859-1"
> 
> On 11/04/2012 7:28 AM, Dmitry Nerukh wrote:
> >
> > Hi,
> >
> > When using MPI, how do I calculate the local atom number from the
> > global one?  The code given here
> >
> >
> http://www.gromacs.org/Developer_Zone/Programming_Guide/Programm
> er%27s_Guide#local_index
> >
> > does not work for the latest gromacs 4.5.5 which I need.  Also, if I
> > understand correctly, the given code only works for domain
> > decomposition.  I need a universal method... Thanks!
> >
> 
> Then you'll have to see how particle decomposition (and current DD) does
> it by looking at the code. It won't be any harder than the snippet there
> suggests. Of course, a static guide will go out of date as the code
changes.
> 
> > My ultimate goal is to hack mdrun such that I can output only a few
> > atoms' positions and velocities, say atoms 0,1, and 3, but fairly
> > frequently (say, every 10 steps).
> >
> 
> nstxtcout, xtc_precision and xtc_grps can solve this problem already.
> 
> Mark
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