Re: Problems on SMD simulation

From: Axel Kohlmeyer (
Date: Fri Dec 26 2008 - 14:31:18 CST

On Thu, 25 Dec 2008, wrote:

CZ> Hello, everyone.

hello clark!
CZ> I want to study the unfolding process of a protein using SMD. I know it's not
CZ> so hard to do it by NAMD. But I got a quesion here. When I carry out the
CZ> simulation, can I use the PME to do with the long-range interaction? You know,

of course you can use PME, why not?

CZ> generally in SMD simulation, one atom in the protein is pulled and the protein
CZ> begin to unfold. Then, The protein maybe become a long peptide that could be
CZ> embeded into a periodical cell(box). Does this affect the results of simulation?

regardless of periodic boundaries or droplet boundaries, you
certainly have to make sure that there are no artefacts due
to the boundary conditions, and that means that the simulation
cell has to be dimensioned accordingly to contain the whole
_unfolded_ molecule with proper safety distance between the
molecule and its peridic images or the droplet boundary.

whether droplet or periodic boundaries are the proper choice
for SMD calculations or MD simulations in general depends a
lot on the system at hand, the level of accuracy that you
are interested in and how much it is affected by other factors.

please note, that droplet boundary condititions and very short
solvation radii are frequently preferred in tutorial examples
for the simple reason that they speed up calculations significantly.

CZ> Furthermore, anyone here can give me some suggestion to avoid this problem??

this is the kind of problem, where every recommendation begins
with "it depends", since a safe recommandation would require
access to practically infinite compute resources. ;)


CZ> Cheers
CZ> Clark

Axel Kohlmeyer
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
If you make something idiot-proof, the universe creates a better idiot.

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