[gmx-users] hydrogens in pope headgroups
qing.zhu at ttu.edu
Fri Jul 29 16:24:27 CEST 2005
Dear gmx users:
I am trying to run simulations on lipid bilayer of complex composition
that contains popc and pope. The problem I have is that the simulation
always crashes within the first 100 steps. The topology files I used for
popc and pope are both from Peter Tieleman's website
(http://moose.bio.ucalgary.ca/), so the topologies should be ok. From
the VMD movie of the crashed simulations, I found the problem was caused
by the high frequency motions of hydrogen atoms in pope headgroups.
Adding "constraints=hhonds" in the .mdp file can keep the simulation
from crashing, but doing this might affect the hydrogen bonding of pope
molecules, which is not what I want. So does anybody have a better way
that does not affect the hbonds in the system?
Thanks a lot.
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