[gmx-users] g_density and g_potential for DMPC bilayer

Andrei Gurtovenko agu at fyslab.hut.fi
Sun Jun 22 17:33:00 CEST 2003

Dear David,

David wrote:

>>You are right, it's possible to re-center bilayer using trjconv,
>>the problem is that one needs to do that for EVERY frame of simulation
>>because COM position of bilayer fluctuates in time.
>>It seems to me that this needs extra coding.
>you may consider using center of mass groups for your next simulation.
>You can then stop the com motion of different groups in your simulation.
Yes, that's right but my current simulations are over, now I'm analyzing 

>>As for the program for determining PN vector of a PC-head,
>>it would be nice to have it, if possible.
>I'm not sure what you're after. Have you checked g_order and g_rotacf
>anf g_bond?
Actually, I want to calculate the orientation of PC groups (angles with 
bilayer normal)
for DMPC bilayer. Not sure that the programs you mentioned help.

Also, I have a question addressed to GROMOCS crew:
Could you tell me whether g_density explicitly takes into account
masses of united-atom carbons supplied in .tpr file
(i.e. it knows whether a carbon is C, CH, CH2 or CH3) .
I heard an opinion that g_density uses atom names instead
and it is necessary to add masses of hydrogens "by hand"?

Thanks in advance,


Dr. A. Gurtovenko

Biophysics and Soft Matter Group
Laboratory of Physics
Helsinki University of Technology
P.O.Box 1100
FIN-02015 HUT
Tel.: +358-9-4515803
e-mail: agu at fyslab.hut.fi

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