[gmx-users] g_density and g_potential for DMPC bilayer

Andrei Gurtovenko agu at fyslab.hut.fi
Fri Jun 20 14:03:00 CEST 2003

Dear Gromacs-users and developers,

I use GROMACS for simulating a DMPC bilayer in water
(united-atom model).

Now I'm analyzing trajectories.
I've got several questions regarding to Gromacs software supplied
for an analysis:

1. g_density.
As I said I use united-atom ff.
Could anybody tell me what EXACTLY g_density does
during mass density calculation:
Whether it uses atom types supplied by .tpr file
and exactly takes into account masses of atoms used in topology,
or it uses atom names instead (i.e. it does not know whether
carbon is C, CH, CH2 or CH3) and it is necessary to add (explicitly)
masses of hydrogens "by hand"?

2. g_density
During simulations I removed a displacement of center of mass
of the whole system "bilayer+water" every time step.
But obviously it does not prevent a COM of bilayer (only) to move.
Now, if I'm going to calculate the mass density profile,
it would be reasonable to exclude such a motion of COM of bilayer
(i.e. to take into account positions of all atoms with respect to
the center of bilayer). Otherwise, the density profile will be 'smeared'
by the motion of COM of bilayer.
As far as I see, such a feature is not implemented in g_density.
Is it possible to take into account the motion of COM of bilayer
somehow in GROMACS? Say, I can easily compute the COM of bilayer
using g_traj -com; but it seems to be no ways to re-insert the
corrected positions back to g_potential

3. g_potential.
The same question as in item (2) also relates to the computation
of electrostatical potential across the box:
Is it possible in GROMACS to take into account the motion of COM
of bilayer when calculating electrostatical potential?

4. I didn't find any ways (in GROMACS) to
calculate orientations of lipid head groups.
Am I wrong?

Thank you in advance,

Andrei Gurtovenko

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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