Re: Re: Protein moving out of box during npt simulation

From: Bjoern Olausson (namdlist_at_googlemail.com)
Date: Tue Jul 05 2011 - 04:22:50 CDT

On Tuesday 05 July 2011 10:40:59 bharat gupta wrote:
> I repeated the nvt equilibration again with cell origin (the actual one),
> but still I am getting the protein going out of the box. But the energy and
> temperature is stable. What shall I do in this case, shall I continue with
> npt simulation without keeping the protein in the center of the box as I
> have taken PBC into consideratioon ???
>

When you are using PBC you don't have to worry about that.
You can recenter the trajectory on the protein and eliminate the protein drift
this way once your simulation is complete.

http://www.ks.uiuc.edu/Research/vmd/plugins/pbctools/
Search for "pbc wrap"

Cheers,
Bjoern

-- 
Bjoern Olausson
Martin-Luther-Universitšt Halle-Wittenberg 
Fachbereich Biochemie/Biotechnologie
Kurt-Mothes-Str. 3
06120 Halle/Saale
Phone: +49-345-55-24942

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