scaling the interaction energy

From: Krishnan, Marimuthu (
Date: Wed May 21 2008 - 07:21:20 CDT

Dear all,

I would like to perform a few MD runs with scaled interactions between set A and B of atoms (different MD runs with different scaling factors). How can do that? NAMD documentation describes about 'nonbondedScaling' but this option scales the nonbonded forces acting in the whole system.

When the nonbonded interactions between set A and B are scaled, the whole system will no more be neutral. How do we keep the system neutral in such cases?

Thanks all.


Dr. Marimuthu Krishnan
Postdoctoral Research Scholar,
Center for Molecular Biophysics,
Oak Ridge National Laboratory,
PO Box 2008 MS6164,
Oak Ridge, TN 37831-6164,
Tel : 001-865-574-6123
Fax : 001-865-576-7651
E-mail :


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