[gmx-users] vsites and lincs-order

[Jochen Hub]

Berk Hess wrote:
>
>
> > Date: Wed, 7 Oct 2009 15:51:00 +0200
> > From: jochen at xray.bmc.uu.se
> > To: gmx-users at gromacs.org
> > Subject: Re: [gmx-users] vsites and lincs-order
> >
> > 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.
> >
>
> grompp you mean, I guess?
>
> > 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.
>
> We can not do such things.
> Gromacs is not a atomistic, protein specific simulations package.
> For other systems, masses, etc. such settings could be fine.
> Moreover, grompp can not easily check for this specific type of vsite use.
> TIP4p, for instance, also contains a vsite.
>
> It has happened that someone put in similar checks in grompp, but this 
> can be
> EXTREMELY annoying when you use different systems.

I see...

Jochen



>
> Berk
>
> >
> > 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
> > ---------------------------------------------------
> >
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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
---------------------------------------------------