[gmx-users] Lipids and virtual site in 4.6.1

David van der Spoel spoel at xray.bmc.uu.se
Mon Apr 8 11:55:29 CEST 2013

On 2013-04-08 11:52, David van der Spoel wrote:
> 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
>> 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
> effect?

And by the way, you are welcome to reopen the redmine issue and upload 
file demonstrating the problem.
>> 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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