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-Universität 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 - 23:20:33 CST