[gmx-users] Gromacs and restraints

Ran Friedman r.friedman at bioc.uzh.ch
Wed Jul 16 17:13:07 CEST 2008

Hi Matteus,

The time step should be smaller than the fastest fluctuations in your
system, which are normally X-H bonds, with frequencies around 10fs. To
be ten times faster, you should use 1fs, which normally gives stable
simulations even if you don't use constraints. If you constrain the X-H
bonds, you get a factor of two more-or-less, so you're fine with 2fs. To
be on the safe side, you can constrain all-bonds. More elaborate methods
allow you to use a larger timestep. IIRC, one of David's lectures in the
GMX workshop in Finland had a slide about it, so you can check
if you're interested.

Good luck,

Matteus Lindgren wrote:
> Hi all
> I´m new to gromacs, having previously worked with Charmm.
> After looking through articles and gromacs tutorials it seems many use
> the SETTLE algorithm for water, restraining both water angle and
> bonds, as well as restraining all bonds in proteins, while using a
> timestep of 2fs. I believe in Charmm it is common practice to only use
> SHAKE on X-H bonds, not angles or X-X bonds, for the same timestep. I
> got curious, why the different setups for the different programs,
> force fields?
> I will be running protein in explicit water simulations and need a
> timestep of 2fs. Forces and energies in the system will be analyzed.
> What restraint setup should I choose?
> Regards
> /Matteus  
> Matteus Lindgren
> Graduate student
> Department of Chemistry
> Umeå University
> SE-901 87 Umeå, Sweden
> Tel: +46 (0)90 786 53 68
> e-mail: matteus.lindgren at chem.umu.se <mailto:barbara.addario at chem.umu.se>

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20080716/dafe6e6c/attachment.html>

More information about the gromacs.org_gmx-users mailing list