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: [EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]> >
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