[gmx-users] virtual sites with CHARMM lipids

Bastien Loubet bastien at memphys.sdu.dk
Thu Dec 20 11:39:24 CET 2012

Dear GROMACS users,

I have been working on a CHARMM36 POPC bilayer and in order to accelerate
the simulation we want to use virtual sites for the hydrogen atoms in the

We mainly want to do it for the carbon tails of the lipids.
I have checked the different type of virtual sites in the GROMACS manual
(3fd, 3fda, 3out, N) but none of them seems to correspond to the CH2 groups
in the carbon chains.
It would require an out of plane virtual site with fixed length (so using
normalized vector).

Can you help me with that ?


Bastien Loubet

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