[gmx-developers] FEP Instability problem

[Shirts, Michael (mrs5pt)]

Hi, David-

I'm happy to take a look at the files.  If you have configurations both
where it's at -600 kJ/mol and -5 kJ/mol, that would make it much easier.

Best,
~~~~~~~~~~~~
Michael Shirts
Assistant Professor
Department of Chemical Engineering
University of Virginia
michael.shirts at virginia.edu
(434)-243-1821


> From: David van der Spoel <spoel at xray.bmc.uu.se>
> Reply-To: Discussion list for GROMACS development <gmx-developers at gromacs.org>
> Date: Fri, 4 Nov 2011 11:38:55 +0100
> To: Discussion list for GROMACS development <gmx-developers at gromacs.org>
> Subject: [gmx-developers] FEP Instability problem
> 
> Dear all,
> 
> I'm trying to FEP away a TIP4P water molecule from a water box in gmx
> 4.5.3, but getting a jump in dH/dlambda after some time (around 100 ps),
> from around -5 to -600 kJ/mol/lambda. I'm using softcore with the
> following parameters:
> 
> sc-alpha = 0.5
> sc-power = 1
> sc-sigma = 0.3
> delta-lambda             = 0
> init-lambda = 0.1
> couple-lambda0 = vdw
> couple-lambda1 = vdw-q
> free-energy              = yes
> 
> I've also tried using
> sc-alpha = 0
> sc-power = 0
> 
> Any clues what could go wrong?
> 
> Could it be due to the virtual sites?
> 
> Although not strictly a developer problem I took the liberty of sending
> this to the developer list anyhow, under the rationale that if a
> developer has problems with simulations, others may have them too, and
> something might need fixing.
> 
> -- 
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
> spoel at xray.bmc.uu.se    http://folding.bmc.uu.se
> -- 
> gmx-developers mailing list
> gmx-developers at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-developers
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-developers-request at gromacs.org.