RE: Harmonic dihedral restraints

From: Jeff Wereszczynski (jmweresz_at_umich.edu)
Date: Mon May 07 2007 - 19:15:30 CDT

Hi Christopher,

 

You have two options that I know of:

 

1.) You can write your own TclForces script to do this. The NAMD
Documentation gives an example on how to restrain the dihedral of four
atoms, so this would be pretty straightforward. Also there is a tutorial on
TclForces that is pretty good and you can check out to get more information.

2.) If you are using Alan Grossfield's WHAM code then you can edit the
calc_bias function to calculate the bias from the sinusoidal function that
is implemented in NAMD rather then the quadratic one that is generally used.
I think all you have to do is edit this function in the histogram.c source
file and you should be set.

 

Hope that helps!

Jeff Wereszczynski

 

  _____

From: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] On Behalf
Of Christopher Rowley
Sent: Monday, May 07, 2007 5:57 PM
To: namd-l_at_ks.uiuc.edu
Subject: namd-l: Harmonic dihedral restraints

 

Hi,

 

I'm trying to calculate the phi-psi free energy surface using NAMD and
wham-2d. wham-2d requires harmonic dihedral restraints, although the
restraints list in the NAMD manual are of a different form. Is it possible
to use harmonic dihedral restraints within NAMD?

 

Alternatively, is there a straightforward way to calculate a phi-psi free
energy surface using NAMD directly?

 

Christopher Rowley

Department of Chemistry

University of Ottawa

 

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