[gmx-users] g_density and g_potential for DMPC bilayer

Xavier Periole Xavier.Periole at physbio.mssm.edu
Mon Jun 23 17:40:02 CEST 2003

Hi  Andrei

> 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.

I don't see where the problem is. You give your trajectory to trjconv
trjconv -f traj.xtc -n index.ndx -o trajout.xtc
because you specify an index, the program asks you the group you
want to center and the group you want as output. So as output you
have your whole system centered on the group you choose. The center
the program chooses is probably geometrical but check on some snapshots
you'll find that it is almost the same as the COM. It would be necessary
to check the code but I am also convinced that the program re-centers
in the box at each frame of the trajectory.

As for the program to get the PN orientation no problem. I'll send you a
copy later today.


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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