Re: need help on CG modelling

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Mon Sep 22 2008 - 12:48:28 CDT

Just to add to what Nicolas said, a few people in the .ks.uiuc.edu
domain are currently working on a full conversion of martini to work
with the namd/vmd toolchain, but it is still being tested and is not yet
ready for public consumption.
Best,
Peter

Nicolas Sapay wrote:
> 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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