________________________________________
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf
of Krzysztof Kuczera [kkucz...@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?
Krzysztof Kuczera
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.
Jan
--
Krzysztof Kuczera
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: kkucz...@ku.edu
http://oolung.chem.ku.edu/~kuczera/home.html
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