Re: need help on CG modelling

From: Nicolas Sapay (nsapay_at_ucalgary.ca)
Date: Mon Sep 22 2008 - 12:34:47 CDT

The Martini force field was initially made to run with Gromacs, not
NAMD. If you want to generate a psf file from it, you must convert the
martini.itp file into a format suited to psfgen/NAMD. I've got a rtf
file for Martini, but it contains topologies only, not parameters for
bonded/non-bonded interactions (I'm using it to generate psf file
readable in VMD, not to run MD simulations. In your case, it is probably
easier to generate a Gromacs topology file and to use it as input to
NAMD (check the NAMD manual, there is a section about that). You should
also check Marrink's website:

http://md.chem.rug.nl/~marrink/coarsegrain.html

There are few tools to "coarse-grain" a system. In all cases, you must
verify that you obtain identical energy values with NAMD and GROMACS
before using your system. If both engines use the same basic equations
to run MD, they don't use the same code and extra-features. So, you
might obtain significant differences if you're not cautious. Regarding
the amount of work it can take, I would consider to directly use
Gromacs, except if you have to use code very specific to NAMD.

Cheers,
-Nicolas

Liao Chuan wrote:
>
> /Hi all,/
>
> /Iím trying to run a residue-based CG MD simulation with NAMD for a
> system which includes waters, proteins, and a lipid bilayer using the
> Martini version2.1 CG force field. (//
> http://pubs.acs.org/cgi-bin/abstract.cgi/jctcce/2008/4/i05/abs/ct700324x.html
> //)/
>
> /However, I have difficulties in preparing the following files for CG:
> pdb file, psf file, parameter file and configuration file. Is there
> any training course on the preparation of those 4 CG files? Or else
> does anyone have sample pdb, psf, parameter, and configuration files
> for CG simulation (like the samples available for standard NAMD
> simulations) and send me a copy ?/
>
> /Any suggestion will be appreciated./
>
> /Best wishes,/
>
> /Chuan Liao///
>


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