[gmx-users] Lipids and virtual site in 4.6.1

David van der Spoel spoel at xray.bmc.uu.se
Mon Apr 8 11:52:50 CEST 2013

On 2013-04-08 11:34, Bastien Loubet wrote:
> Dear GROMACS user,
> Last week I was watching the GTC talk from Eric Lindahl, and I noticed his
> insistence on virtual site to accelerate simulation (up to 5ps time step).
> As a matter of fact our group recently tried to use virtual site on CHARMM36
> POPC bilayer and the result where less than stellar.
> We first did a simulation of a POPC bilayer comparing area per lipid with
> and without virtual site using GROMACS 4.5.5.
> We obtained an area per lipid around 0.62 nm^2 per lipid with no virtual
> site but with virtual site we obtained an area per lipid of more than 0.7
> nm^2.
> After that we found that there was a bug report for the virial calculation
> with virtual site in version 4.5: http://redmine.gromacs.org/issues/908
> The issue being marked as resolved for 4.6 and we tried our hand at both the
> beta3 and 4.6.1 version of it. The result where better but not perfect: we
> get 0.65~0.66 nm^2 per lipid.
> The problem here is that in order to increase the time step we need all
> hydrogen to be virtual sites, so this include the lipids hydrogen and not
> just the protein. However if the area per lipid is wrong the stress profile
> is likely to be changed, which will affect transmembrane proteins. So we do
> not feel confident about using virtual sites in our lipid simulation.
> I signal it here because there is a possibility that this is still a bug, If
> somebody could confirm/infirm that it would be nice.

Did you also try to use vsites without increasing the time step, in 
order to rule out that this is a time step effect rather than a vsite 

> Best,
> Bastien
> --
> View this message in context: http://gromacs.5086.n6.nabble.com/Lipids-and-virtual-site-in-4-6-1-tp5007063.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.

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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