[gmx-users] Discrepancy between Free Energy Perturbation usingGromos96 and OPLS
ssomani at bii.a-star.edu.sg
Tue Oct 4 11:56:33 CEST 2005
Adding to that, as per David's suggestion, I installed gmx3.3_rc3 and
ran the same simulation again.
The values are still similar i.e. ~ -30kJ/mol for Gromos96 and <
-300kJ/mol for OPLS.
I tried again with PME too .. still the OPLS values are much lower than
am quite clueless now ! ill be happy to provide the input files if
anyone wants to probe further ..
> -----Original Message-----
> From: gmx-users-bounces at gromacs.org
> [mailto:gmx-users-bounces at gromacs.org] On Behalf Of Maik Goette
> Sent: Tuesday, October 04, 2005 5:41 PM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] Discrepancy between Free Energy
> Perturbation usingGromos96 and OPLS
> Hi David
> 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
> 37077 Goettingen
> 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/
> David wrote:
> > 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
> >>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
> > 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
> >>gmx-users mailing list
> >>gmx-users at gromacs.org
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