[gmx-developers] FEP Instability problem
Shirts, Michael (mrs5pt)
mrs5pt at eservices.virginia.edu
Fri Nov 4 13:38:07 CET 2011
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.
Department of Chemical Engineering
University of Virginia
michael.shirts at virginia.edu
> 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
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