[gmx-users] Microcanonical MD with PBC
David van der Spoel
spoel at xray.bmc.uu.se
Tue Jul 15 09:21:06 CEST 2008
Lee-Ping Wang wrote:
> Hi everyone,
> I've been trying to get a microcanonical (energy conserving, NVE) MD run
> with periodic boundary conditions. I'm using the provided box of 216
> water molecules and the SPC force field (flexible). When I turn PBC
> off, the energy RMSD is <0.01kJ/mol with a 0.1fs time step (energy is
> conserved). When PBC is turned on, the energy RMSD is much greater at
> ~50kJ/mol. Even when I turn off the atomic charges, the energy RMSD is
> still the same, so I am suspecting that at least the VdW potential
> switching methods is at fault.
Did you try shifting instead of switching? See also JCTC 2 pp. 1-11
(2006) for a comparison of (some of the) different shift/switch
functions in different packages, including some never-before published
trade secrets :).
> Anyone able to help?
> Here are the relevant parameters in the mdp file...
> nstlist = 1
> ns_type = grid
> rlist = 0.9
> coulombtype = pme
> vdwtype = switch
> rcoulomb = 0.9
> rvdw = 0.8
> rvdw_switch = 0.5
> constraints = none
> pbc = xyz
> tcoupl = no
> gen_vel = yes
> gen_temp = 300
> gen_seed = 173529
> Thanks a lot,
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David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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