[gmx-users] vsites and lincs-order

Berk Hess gmx3 at hotmail.com
Wed Oct 7 14:34:29 CEST 2009

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.


> 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
> ---------------------------------------------------
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
What can you do with the new Windows Live? Find out
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20091007/400ae021/attachment.html>

More information about the gromacs.org_gmx-users mailing list