[gmx-users] g_density CHARMM
rguixa at imim.es
Wed Jan 12 00:46:50 CET 2011
Thanks again Justin
From: Justin A. Lemkul <jalemkul at vt.edu>
Reply-to: "jalemkul at vt.edu" <jalemkul at vt.edu>, Discussion list for
GROMACS users <gmx-users at gromacs.org>
To: Gromacs Users' List <gmx-users at gromacs.org>
Subject: Re: [gmx-users] g_density CHARMM
Date: Tue, 11 Jan 2011 22:08:22 +0100
Ramon Guixà wrote:
> Thanks for your response.
> The membranes I've already run are made of POPC and cholesterol, so the
> sphingomyelin membrane is my next simulation but I haven't managed to
> find a proper forcefield for it. Would you know where to find this?
Not for CHARMM, no, but there are several available for different Gromos force
http://www.apmaths.uwo.ca/~mkarttu/downloads.shtml (contact Prof. Karttunen for
> -----Original Message-----
> *From*: Justin A. Lemkul <jalemkul at vt.edu
> <mailto:%22Justin%20A.%20Lemkul%22%20%3cjalemkul at vt.edu%3e>>
> *Reply-to*: "jalemkul at vt.edu" <jalemkul at vt.edu>, Discussion list for
> GROMACS users <gmx-users at gromacs.org>
> *To*: Discussion list for GROMACS users <gmx-users at gromacs.org
> <mailto:Discussion%20list%20for%20GROMACS%20users%20%3cgmx-users at gromacs.org%3e>>
> *Subject*: Re: [gmx-users] g_density CHARMM
> *Date*: Tue, 11 Jan 2011 19:45:58 +0100
> 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!
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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