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: 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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