j.marzinek10 at imperial.ac.uk
Wed May 2 21:08:08 CEST 2012
From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] on behalf of Krzysztof Kuczera [kkuczera at ku.edu]
Sent: Wednesday, May 02, 2012 6:38 PM
To: Discussion list for GROMACS users
Subject: [gmx-users] pullf.xvg
Could someone please tell me what exactly is printed in the pullf.xvg
file from an umbrella sampling simulation?
Is it the total force acting the COM of the pull group - i.e. force from
regular potential plus the umbrella force or just the unbiased force?
Each window in umbrella sampling simulation gives you the biased potential which is the harmonic potential. The wham allows you to combine all windows by applying weights and calculating the unbiased potential which requires calculation of the free enerrgy associated with introducing the harmonic pontial (biased). Please, search literature to see equations.
Departments of Chemistry and Molecular Biosciences
The University of Kansas
2010 Malott Hall
Lawrence, KS 66045
Tel: 785-864-5060 Fax: 785-864-5396 email: kkuczera at ku.edu
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