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

[Frankie Montenegro]

Thanks guys. I guess I'll be running it again. I only deshuffled 3) to 4)

On 9/14/07, Yang Ye <leafyoung at yahoo.com> wrote:
> On 9/14/2007 5:35 PM, steletch at jouy.inra.fr wrote:
> > 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
> >
> Instead, -shuffle and -sort will all disappear in the next version. I
> encourage Frankie to benchmark the speed-up ratio, especially it is not
> a membrane system. I know that people would not use -sort/shuffle so as
> not to mess things up for some "little" lost in speed. That's just alright.
> >> 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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