[gmx-users] Microcanonical MD with PBC

[David van der Spoel]

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,
> Lee-Ping
> 
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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