Re: Help with SMD

From: Richard Law (rlaw_at_hanyou.llnl.gov)
Date: Wed Jul 20 2005 - 10:54:50 CDT

Prior to the production run of any simulation you need to do a run with
the position of the protein restrained, with pressure coupling on, to
equilibriate the rest of system. Otherwise this will happen and your
results will be rubbish.

On Tue, 19 Jul 2005, Eunice Ramirez Melendez wrote:

>
> Hi all
>
> I am running a constant velocity SMD and I have some unexpected results during the simulation. If my equilibrated
> system has PBC (with vectors 30 x30 x 120) it is normal that during the simulation the rectangular properties of the
> system are lost? After a couple of ps the solvent has moved and create an environment similar to the sphere in NPBC. I
> do not know if this is normal. Do I need to use a NPB equilibarated system to run a SMD? Please help me!!!
>
> Thanks, Eunice
>
> -------------------------------------------------------------
> Antes ahora y siempre COLEGIO
> University of Puerto Rico at Mayaguez
> http://www.uprm.edu
> -------------------------------------------------------------
>
>

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