Re: Coarse-grained Modeling/User defined FF

From: Peter Freddolino (
Date: Thu Mar 29 2007 - 13:23:17 CDT

Hi Josh,
I think the reason that there isn't much documentation is that it's very
problem dependent. A lot of CG simulations just use a charmm style
forcefield, in which case no modifications to NAMD are necessary. Small
changes to the forcefield, such as changing the form of a bond or angle
potential, can be done pretty easily in your own version (these are
computed in ComputeAngle.C and the like). Likewise, if you have a change
in the nonbond potential you'd need to modify ComputeNonbondedBase2.h
and replace the LJ potential with what you want. To allow people to use
arbitrary nonbond potentials, I'm currently in the process of adding
energy lookup tables to NAMD, but this is only necessary for a subset of
CG simulations. If you have more specific questions about exactly what
sort simulation you want to set up, people on the list may be able to help.

Joshua Adelman wrote:
> I have been reading with great interest the papers on using NAMD to do
> coarse-grained simulations. I was wondering if there was documentation
> on how to set up those sorts of problems and how to modify NAMD to
> handle user-defined force fields that one might need to add in a
> coarse-grained simulation? I have searched the web and the archives of
> the NAMD lists and haven't found any specific resources addressing
> this issue.
> Thanks in advance for any suggestions.
> Josh
> ------------------------------------------------------------------------------------------------------
> Joshua L. Adelman
> Biophysics Graduate Group Lab: 510.643.2159
> 218 Wellman Hall Fax: 510.642.7428
> University of California, Berkeley
> <>
> Berkeley, CA 94720 USA
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