Re: need help on CG modelling

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Mon Sep 22 2008 - 14:24:09 CDT

Hi Nicolas,
I hate it when people give noncommittal answers like "when it's ready".
But that's pretty much it -- or more accurately, as soon as we're
convinced that everything works correctly by reproducing the data from
the martini papers. Everything is being tested now, so I wouldn't expect
more than a couple weeks, but I hate to give firm estimates when doing
this type of work because one always seems to run into more difficulties
than one expects.
Peter

Nicolas Sapay wrote:
> 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///
>>>>
>>>
>>
>>
>

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:49:51 CST