[gmx-users] g_density and g_potential for DMPC bilayer

Andrei Gurtovenko agu at fyslab.hut.fi
Sun Jun 22 17:01:02 CEST 2003

Dear Xavier,

thanks for your advices.

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.

As for the program for determining PN vector of a PC-head,
it would be nice to have it, if possible.



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

Xavier Periole wrote:

>dear Andrey,
>you can recenter your bilayer using trjconv -center -n index.ndx
>in the index you'll should have a group been your bliayer. 
>For the orientation of the head groups I have a program that
>determines the angle of the PN vector (or what ever pair of atoms)
>relative to the z axis. That is probably what you need. So if you 
>want it, tell me.
>Xavier Periole, Ph.D.
>Chemistry Dept. 
>City College of New York (CUNY)
>138th St. and Couvent Av.
>New York, NY 10010
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>gmx-users at gromacs.org
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