[gmx-users] g_density CHARMM

Justin A. Lemkul jalemkul at vt.edu
Tue Jan 11 19:45:58 CET 2011

Ramon Guixà wrote:
> Dear all,
> I am just a newbie to Gromacs so sorry for being naive with my questions...
> 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?

Not likely.  pdb2gmx is useful for creating topologies of macromolecules built 
of repeating units (i.e. proteins and polymers).  For lipid bilayers, it is far 
more common to construct the topology as a set of #include statements, i.e.:

#include (forcefield)

#include "first_lipid_type.itp"
#include "next_lipid_type.itp"


> 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?

Newer versions of Gromacs (>4.5) can read any file format that VMD can read, so 
conversion is not necessary, provided you have the VMD libraries installed.

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

If you already ran the simulations, do you not already have this?  With the 
information in Chapter 5 of the manual, you should be able to convert your 
topologies from whatever format you have it in into the one required by Gromacs.


> Many thanks in advance!
> Ramon


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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