[gmx-users] Discrepancy between Free Energy Perturbation usingGromos96 and OPLS
Mu Yuguang (Dr)
YGMu at ntu.edu.sg
Sun Oct 2 15:21:03 CEST 2005
Although I have done the work as you did. But from the quite different
partial charges set used by the two force fields, it is not surprised to
have such different results. Usually the free energy calculation depends
on charges greatly.
The more important thing is to check your convergence of your simulation
to validate your results.
Dr. Yuguang Mu
Division of Structural and Computational Biology
School of Biological Sciences
Nanyang Technological University
60 Nanyang Drive
From: gmx-users-bounces at gromacs.org
[mailto:gmx-users-bounces at gromacs.org] On Behalf Of Sandeep Somani
Sent: Saturday, October 01, 2005 1:12 PM
To: gmx-users at gromacs.org
Subject: [gmx-users] Discrepancy between Free Energy Perturbation
usingGromos96 and OPLS
I did a Slow Growth (dummy -> real) based FEP of a small ligand bound to
a protein using Gromos and OPLS ff.
Description of ligand in both cases is identical.
Free energy change from the Gromos simulation is reasonable but the
number from OPLS is an order of magnitude more negative.
All parameters (reaction field electrostatics, constraints in topology,
delta-lambda etc) other than the ff are identical. Am using gmx3.2.1.
Has anyone encountered this before ? what could be the origin of this
Thanks and Regards
Computational Biology Group
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