Re: alchemical fep amber topology

From: Floris Buelens (floris_buelens_at_yahoo.com)
Date: Sat Mar 14 2009 - 05:53:37 CDT

Hi George,

In principle this is absolutely fine in both released and CVS versions of NAMD - just do everything according to the tutorial, but with "amber on" and "parmfile" instead of a PSF file. However, there is as yet no equivalent to 'alchemify' for parm7 files. This is only an issue if you're working with dual topology alchemical groups that are bonded to the rest of the system (e.g. a dual topology residue definition) - for groups that aren't bonded to the rest of the system everything should work as you would expect without modifying the parm7.

Floris

----- Original Message ----
From: George Madalin Giambasu <giambasu_at_gmail.com>
To: namd-l_at_ks.uiuc.edu
Sent: Friday, 13 March, 2009 18:55:22
Subject: namd-l: alchemical fep amber topology

Hi,

I was wondering if there is a way to run alchemical fep simulations
using Amber topologies (*.parm7 files) using the cvs version of namd?

I found a post by Jerome Henin
(http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/1348.html) on
the list in which it was stated that the fep setup "does not need CHARMM
anymore", however the Alchemical FEP tutorial states that we have to use
psf files in conjunction the alchemify program.

Thanks in advance for any suggestions or updates!

George

      

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