Re: need help on CG modelling

From: Nicolas Sapay (nsapay_at_ucalgary.ca)
Date: Mon Sep 22 2008 - 13:59:16 CDT

Peter Freddolino wrote:
> 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
>
That would be great! I was planning to code some conversion tools, but
VMD/NAMD people will probably do a better job than me. Do you have an
idea when their work will be available? I'd like to test the pressure
profile calculation in the NAMD code.

Nicolas

> 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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