RE: Help with SMD

From: Michel Espinoza-Fonseca (
Date: Wed Jul 20 2005 - 11:18:31 CDT

Richard is right. You can find useful scripts to minimize, warm up and
equilibrate your system at:

I have to warn you that you should modify some parts of the scripts in
order to obtain accurate results (for example, disable the flexible

-----Original Message-----
From: [] On
Behalf Of Richard Law
Sent: Wednesday, July 20, 2005 10:55 AM
To: Eunice Ramirez Melendez
Subject: Re: namd-l: Help with SMD

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
> -------------------------------------------------------------

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