[gmx-users] Discrepancy between Free Energy Perturbation usingGromos96 and OPLS

[Sandeep Somani]

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
Gromos. 

am quite clueless now ! ill be happy to provide the input files if
anyone wants to probe further .. 

Regards
Sandeep 




> -----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. :)
> 
> Regards
> 
> Maik Goette, Dipl. Biol.
> Max Planck Institute for Biophysical Chemistry
> Theoretical & computational biophysics department
> Am Fassberg 11
> 37077 Goettingen
> Germany
> Tel.  : ++49 551 201 2310
> Fax   : ++49 551 201 2302
> Email : mgoette[at]mpi-bpc.mpg.de
>          mgoette2[at]gwdg.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 
> >>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
> >>Sandeep
> >>
> >>---
> >>Research Associate
> >>Computational Biology Group
> >>Bioinformatics Institute
> >>Singapore
> >>
> >>http://web.bii.a-star.edu.sg/~ssomani/
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
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