Re: ABF tutorial

From: Chris Chipot (
Date: Mon Jul 20 2009 - 09:09:57 CDT


the ABF tutorial assumes, perhaps erroneously so, that the user is
capable, given a PSF and a PDB file, of running an equilibration.
Not being sure of this assumption, we have, nonetheless, provided in
a separate directory, two "vanilla" NAMD configuration files written
for the purpose of energy-minimization and equilibration.


Chris Chipot

sudipta a écrit :
> Hi All,
> I want to run ABF simulation of decaalanine that has given in tutorial
> file. But I have not got all the required file in tutorial directory.
> The files which I have not got are
> coordinates reference_0.coor
> bincoordinates reference.coor
> velocities reference_0.vel
> binvelocities reference.vel
> Can anyone please suggest me where from I get or generate these file.
> Thanks & regards
> Sudipta


Chris Chipot, Ph.D.
on leave from Nancy Université, CNRS
Theoretical and Computational Biophysics Group
Beckman Institute
University of Illinois at Urbana-Champaign
405 North Mathews Phone: (217) 244-5711
Urbana, Illinois 61801 Fax: (217) 244-6078


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