[gmx-users] Lateral Diffusion of Lipids

Jochen Hub jhub at gwdg.de
Wed Aug 14 11:34:34 CEST 2013

Am 8/12/13 5:26 AM, schrieb Kieu Thu Nguyen:
> Dear users,
> I want to use g_msd to measure diffusion coefficients of lipid bilayer. But
> i do not know how to choose the reference atom per lipid for an any type of
> lipid, such as POPC, DOPC,...
> Where i can get these references ?

One suggestion: The two leaflets may move with respect to each other.
Therefore, I recommend to compute D *within* each leaflet first -
otherwise you may get a too large diffusion constant. Btw: g_select can
be used to select the upper / lower phosphates into separate index groups.


> Thanks so much for any help !
> ~Thu

Dr. Jochen Hub
Computational Molecular Biophysics Group
Institute for Microbiology and Genetics
Georg-August-University of Göttingen
Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany.
Phone: +49-551-39-14189

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