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

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
> 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
>

This archive was generated by hypermail 2.1.6 : Mon Dec 31 2012 - 23:20:32 CST