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

From: Bjoern Olausson (namdlist_at_googlemail.com)
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.

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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