[gmx-users] Discrepancy between Free Energy Perturbation using Gromos96 and OPLS
spoel at xray.bmc.uu.se
Sat Oct 1 08:57:17 CEST 2005
On Sat, 2005-10-01 at 13:11 +0800, Sandeep Somani wrote:
> hi all
> 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
> discrepancy ?
It could be due to the all-atom/united atom difference in combination
with the reaction field. Berk has recently implemented an exclusion
correction for reaction fields that could be important here. You could
retry it with 3.3beta to see whether there is a difference.
> Thanks and Regards
> Research Associate
> Computational Biology Group
> Bioinformatics Institute
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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