[gmx-users] Discrepancy between Free Energy Perturbation using Gromos96 and OPLS
mgoette at mpi-bpc.mpg.de
Tue Oct 4 11:40:39 CEST 2005
Could you be a bit more precise?
Is this difference due to a problem of united atoms/reaction field or
all atoms/reaction field. For I also use FEP with all atoms
(amber99-port) and reaction field, I could use some info. :)
Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
Tel. : ++49 551 201 2310
Fax : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/
> On Sat, 2005-10-01 at 13:11 +0800, Sandeep Somani wrote:
>>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
> 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
>>Computational Biology Group
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