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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