From: snoze pa (snoze.pa_at_gmail.com)
Date: Tue Jul 05 2011 - 10:00:23 CDT
Increase the margin and minimize for atleast 20000 steps. Also Make sure
that protein is well equilibrated(do it atleast 2ns).
On Tue, Jul 5, 2011 at 4:22 AM, Bjoern Olausson <namdlist_at_googlemail.com>wrote:
> 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
> > temperature is stable. What shall I do in this case, shall I continue
> > 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
> this way once your simulation is complete.
> Search for "pbc wrap"
> 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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