RE: Help with SMD

From: Blake Charlebois (
Date: Wed Jul 20 2005 - 11:10:47 CDT

Hi Eunice,

I am not sure whether I understand what you have described, but it sounds as
though either your water coordinates are not wrapped (this is neither good
nor bad, see coordinate wrapping in the NAMD manual), or you are turning off
your periodic boundary conditions after equilibration (this does not strike
me as a good idea; as soon as you turn off the periodic boundary conditions,
the system is no longer in equilibrium, which defeats the purpose of
equilibration). You can do SMD in a periodic box if you make the box long
enough in the pulling direction (see Gao, Craig, Vogel, Schulten, J. Mol.
Biol. 323:939, 2002).


-----Original Message-----
From: [] On Behalf
Of Eunice Ramirez Melendez
Sent: July 19, 2005 1:09 PM
Subject: namd-l: Help with SMD

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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