> Date: Wed, 7 Oct 2009 15:51:00 +0200
> From: joc...@xray.bmc.uu.se
> To: gmx-users@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.
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: joc...@xray.bmc.uu.se
> > > To: gmx-users@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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