Re: CG modeling using NAMD

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Sat Nov 22 2008 - 20:49:22 CST

Hi Bin,
for choosing a CG method I'd recommend looking at the relevant
references; the first papers to use both would be:
RBCG: J Phys Chem B, 2006, 110, 3674-3684
SBCG: Structure, 2006, 14, 1767-1777

Both have been significantly refined since then. They differ in terms of
how coarse the CG model actually is.

If you end up wanting to use the RBCG model it's probably better to wait
on on the MARTINI implementation. It has ended up taking longer than I'd
anticipated due to various snags; I believe it's getting pretty close
though, and I'll be sure to let people know when it's done.
Best,
Peter

BIN ZHANG wrote:
> 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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> -------------------------------------------------------------
> The tree of liberty must be refreshed from time to time with the blood
> of patriots and tyrants.
>

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