CG modeling using NAMD

From: BIN ZHANG (zhngbn_at_gmail.com)
Date: Sat Nov 22 2008 - 18:54:05 CST

Hi, All:
     I was thinking about coarse graining my simulation system to run
it faster, then I did a little search find VMD provide 2 CG methods:
RBCG, and SBCG. Could anyone comment a few words on what the
differences between the 2 methods, and what I should consider to make
a wise choice from 1 of them? It seems to me that SBCG is more
applicable to larger system, and also probably more rough?
     Also, I saw the cited mail below on the mailing list and wonder
how this part of work is going on?
Thanks a lot.
Bin

On Sep 22, 2008, at 12:24 PM, Peter Freddolino wrote:

> 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///
>>>>>
>>>>
>>>
>>>
>>
>

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