[gmx-users] Microcanonical MD with PBC

Lee-Ping Wang leeping at MIT.EDU
Mon Jul 14 14:41:30 CEST 2008

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.

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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