[gmx-users] vsites and lincs-order

[Jochen Hub]

All right, thanks!

Since you mention energy conservation, maybe it would be worth adding 
notes or a warnings into pdb2gmx if the time step is large. First, if 
lincs-order is 4 (instead of 6) and second (more important), if nstlist 
is not reduced with increasing dt. I strongly feel that most people who 
use vsites forget to reduce nstlist accordingly.

I have played a bit with timestep and nstlist and checked the energy 
drift - apparently neighbor searching should be done at least every 
20fs. With less frequent neighbor searching the energy drift increases 
drastically (with PME and LJ-cutoff, what people typically use). Now 
imagine a time step of 5fs, with the standard nstlist=10, yields 
neighbor searching only every 50fs. In my test system that increased the 
energy drift by a factor of 10-20 compared to the case where neighbor 
searching was done every 20fs.

Jochen


Berk Hess wrote:
> My P-Lincs paper http://dx.doi.org/10.1021/ct700200b shows that
> with order 6 and a time step of 4 fs you get roughly the same 
> constraint accuracy
> and energy conservation as without v-sites and a 2 fs time step.
> With order 4 and a 4 fs time step the energy drift is 2.2 times higher 
> than with order 6
> (not mentioned in the paper). This is not a very large difference.
>
> I recall that some time ago I decided to change the default lincs 
> order to 6
> (I have not done this yet), but unfortunately now I don't recall what 
> issue
> made me decide that the current default accuracy is not high enough.
>
> Berk
>
> > Date: Wed, 7 Oct 2009 13:16:52 +0200
> > From: jochen at xray.bmc.uu.se
> > To: gmx-users at gromacs.org
> > Subject: [gmx-users] vsites and lincs-order
> >
> > Hi,
> >
> > the manual suggests lincs-order = 6 when using large time steps (4-5 
> fs,
> > with vsites). Has anyone experience how severe that issue is. Has 
> anyone
> > observed artefacts with lincs-order=4 and large time steps?
> >
> > Thanks a lot,
> >
> > Jochen
> >
> > --
> > ---------------------------------------------------
> > Dr. Jochen Hub
> > Molecular Biophysics group
> > Dept. of Cell & Molecular Biology
> > Uppsala University. Box 596, 75124 Uppsala, Sweden.
> > Phone: +46-18-4714451 Fax: +46-18-511755
> > ---------------------------------------------------
> >
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-- 
---------------------------------------------------
Dr. Jochen Hub
Molecular Biophysics group
Dept. of Cell & Molecular Biology
Uppsala University. Box 596, 75124 Uppsala, Sweden.
Phone: +46-18-4714451 Fax: +46-18-511755
---------------------------------------------------