Re: Replica Exchange MD using Amber parameters

From: Kramer Campen (
Date: Thu Jan 11 2007 - 17:14:46 CST

Hey Mark:

I've been experimenting with this a bit and it appears that your statement
isn't true. That is, you can run your replica exchange simulation using
the usual "amber yes" and "parmfile" commands. The existing
scripts to display the results require a psf file so this would require
additional modification but as far as actually generating the data it
appears that you can use Amber parameters in Amber format easily.


At 09:15 AM 1/12/2007 +1100, Mark Abraham wrote:
> > Hey Folks:
> >
> > I'd like to run some replica exchange simulations in NAMD using AMBER
> > parameters. Does anyone have any experience doing this? Could anyone
> > give
> > me any insight into what I'd to alter in order to make this happen?
>You'd need the AMBER parameters expressed in CHARMM format, and thereafter
>probably everything else will be the same.

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:44:18 CST