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

From: Bjoern Olausson (
Date: Fri Jul 08 2011 - 02:50:29 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 ???

How large is your protein (number of AS and max size) and how large is you
water box?
How much does the C.O.M of the protein move in lets say a nanosecond?

But as I previously said, if you are using PBC I wouldn't worry to much, you
can eliminate the diffusion once your simulation is done.


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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