[gmx-users] hydrogens in pope headgroups

Qing Zhu 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.
Qing Zhu

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