Re: Question regarding SMD

From: Leandro Martínez (
Date: Mon Oct 31 2005 - 17:26:23 CST

Dear Glen,

> 1. How can I apply the external force to one particular atom in the ligand
> while I set all atoms in the ligand as SMD atoms?

The SMD atoms are the atoms you are pulling. If you pull a single atom
of your ligand, the whole ligand will dissociate because of the
intramolecular potentials that bind the atoms within the ligands. If
you choose all the ligand atoms to be SMD atoms you will be pulling
the ligand's center of mass. In my SMD simulations I have to choose
pulling one atom because this results in a better definition of the
path, but other choices are reasonable depending on the system under

> 2. How can I choose the pulling direction based on the unbinding path I
> designed?

Well, if you have already designed the path, and it can be
approximately described as a straight line, just choose the pulling
direction as vector parallel to that straight line and pointing to the
outside. The ligand will follow approximately that path, and you
should pull it as gentler as possible in order that the interactions
along the dissociation path are well described, but that depends on
your computational capacity.

Hope it helps,

Leandro Martinez
Institute of Chemistry
State University of Campinas, Brazil

> Grace
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