[gmx-users] To deshuffle or not to deshuffle, that is a question.

[steletch at jouy.inra.fr]

Selon Yang Ye <leafyoung at yahoo.com>:

> Deshuffling shall be made before 2), 3) and 4).

Furthermore, be aware that if you use the 'sort' option, you'll also need to
desort ...
IIRC, there is a g_desort program that does all in one (it was published on the
list some time ago), and should be avaialbe in next gromacs version.

Stéphane

> On 9/14/2007 11:36 AM, Frankie Montenegro wrote:
> > Hi guys,
> >
> > A stupid question: I got myself confused with this
> > shuffling/deshuffling thing, which I
> >  shouldn't have been doing with protein in the first place. So this
> > are my steps, done
> >  on the same 4 nodes, please tell me whether I was supposed to do any
> > deshuffling
> >  of .trr and .gro files, and following which steps:
> > 1)minimization, supplied output .gro to the next step
> > 2)equilibration, supplied output .gro to the next step
> > 3) NVT run, supplied output .gro and .trr to the next step
> > 4) NPT run
> >
> > A simple YES or NO for each step will suffice.
> >
> > Thanks,
> > Frankie
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