[gmx-users] Gromacs and restraints

[Ran Friedman]

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
http://www.csc.fi/english/research/sciences/chemistry/courses/gmx2007/index_html
if you're interested.

Good luck,
Ran.

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>
>

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