[gmx-users] g_density CHARMM

Ramon Guixà rguixa at imim.es
Tue Jan 11 19:23:48 CET 2011

Dear all,

I am just a newbie to Gromacs so sorry for being naive with my

I would like to yield electron density profiles out of different
trajectories of membranes simulated with NAMD and last CHARMM forcefield
(all_36_lipid_cholesterol). I first tried to use pdb2gmx in order to
generate a GROMACS topology file that I could use for generating
the .tpr file needed for g_density. Well, I did not manage but is this
the proper way though?
Also, so far all my trajectories are .dcd files; does the g_density
function needs a .pdb file per frame? Otherwise, is it possible to
directly convert .dcd files into the gromacs .xtc ones?

On another note, would anyone know where could I get proper topology and
parameter files of sphingomyelin?

Many thanks in advance!


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