Re: vmd-l: CG bead definition

From: Anton Arkhipov (anton_at_ks.uiuc.edu)
Date: Tue Nov 25 2008 - 15:31:45 CST

Hi Bin,

>
> I have learned that NAMD and GROMACS have different definition of
> non-bonded interaction, and in order to run CGMD, a little
> modification of NAMD is needed. I wonder whether that's still
> necessary for using your new parameter file: rbcg-2007.par?
That's right, there is a difference, but it is taken into account in
the parameter file that I gave you. That parameter file is CHARMM-
style, so the values of the parameters in that file are different from
the values listed in the original papers by Marrink et al. (they used
GROMACS style). But, the actual potentials are the same, so, to this
end, no modification of NAMD is needed, just use the file I sent you.

By the way, we've just added these files to the RBCG plugin of VMD in
the CVS version, and they should be available in the next VMD release.

One additional remark here is about BONDED potentials. In GROMACS, one
can use cosine-based potential for angles, rather than a harmonic
potential that is used normally by CHARMM-style force-field. Because
of that, we have cosine-based angular terms in the RBCG model (and in
the parameter file I gave you), and we had to use a special version of
NAMD to simulate those. Right now, this can be done with the CVS
version of NAMD. A question about this has been just answered
yesterday on the NAMD mail list by Peter Freddolino, please see below:

On 24 Nov 2008, at 21:17, Peter Freddolino wrote:
> Hi Jani,
> you will need to use the cvs version of namd for now; you can then
> use the flag
> cosangles on
> and appropriately flagged angles in the parameter file will be
> treated with a cosine term.
> Best,
> Peter
>
> jani sahil wrote:
>> Hi all,
>> I read the papers regarding CGMD specially residue based coarse
>> grain modelling ,is it necessary that we need to change
>> some parameters of namd while doing CGMD or the normal NAMD can be
>> used (it is mentioned in paper that cosine based angle parameter is
>> used to modify namd).
>> Right now i am using namd-2.6.
>>
>> any suggestion is welcome
>>
>> regards
>> jani
>

Best,

Anton.

On 25 Nov 2008, at 15:01, BIN ZHANG wrote:

> Hi, Anton:
>
> Thank you so much for those wonderful files. Now I am able to
> coarse grain my system successfully.
> However, before running the simulation, I have another question.
> I have learned that NAMD and GROMACS have different definition of
> non-bonded interaction, and in order to run CGMD, a little
> modification of NAMD is needed. I wonder whether that's still
> necessary for using your new parameter file: rbcg-2007.par?
> Thanks again.
>
> Bin
>
>
>
> On Nov 25, 2008, at 9:44 AM, Anton Arkhipov wrote:
>
>> Hi Bin,
>>
>> I am sending you topology and parameter files for the RBCG model.
>> They contain data for water, as well as for other types of
>> molecules - protein, lipids, and ions.
>>
>> Anton.
>>
>>
>> <rbcg-2007.top>
>>
>> <rbcg-2007.par>
>>
>>
>>
>> On 24 Nov 2008, at 19:13, BIN ZHANG wrote:
>>
>>> Hi, Anton:
>>> Could you also provide me the CG water.top file?
>>> Thanks.
>>> Bin
>>>
>>>
>>>
>>> On Nov 24, 2008, at 4:39 PM, Anton Arkhipov wrote:
>>>
>>>> Hi Bin,
>>>>
>>>> Here are the files.
>>>>
>>>> cgsolvate.tcl is the solvate plugin of VMD that has been tweaked
>>>> to use CG water instead of the all-atom water. The PDB and PSF
>>>> files I am sending are for a box of CG water.
>>>>
>>>> Actually, you should be able to use normal solvate plugin in VMD
>>>> with these PDB and PSF files. I think the solvate GUI in VMD now
>>>> allows you to use non-standard solvent, such as the CG water,
>>>> instead of the all-atom water. You just need to have a PSF and
>>>> PDB files for a box of such a solvent.
>>>>
>>>> Best,
>>>>
>>>> Anton.
>>>>
>>>>
>>>> <cgsolvate.tcl>
>>>>
>>>> <cgwat.pdb>
>>>>
>>>> <cgwat.psf>
>>>>
>>>>
>>>>
>>>>
>>>> On 24 Nov 2008, at 18:24, BIN ZHANG wrote:
>>>>
>>>>> Hi, Anton:
>>>>> Thanks a lot for your help.
>>>>> I also have another question: to coarse grain water molecules
>>>>> using CG builder plugin under GUI, do I still need to run
>>>>> prepare_water explicitly? I ran the CG builder blindly at first
>>>>> and seemed to get wrong results.
>>>>> However, when I try to run prepare_water in command line:
>>>>> mol load pdb water.pdb
>>>>> source $dir/cgtools.tcl
>>>>> ::cgtools::prepare_water 0
>>>>> I ran into memory leak problem, which means I always run out of
>>>>> memory before finishing. ( the total water molecules is 24,000)
>>>>> Do you have any idea what's going on or could you tell what's
>>>>> the right procedure to coarse grain water molecules?
>>>>> Thanks a lot.
>>>>> Bin
>>>>>
>>>>>
>>>>>
>>>>> On Nov 24, 2008, at 2:45 PM, Anton Arkhipov wrote:
>>>>>
>>>>>> Hi Bin,
>>>>>>
>>>>>> Here are two sample files. You should be able to create such
>>>>>> file for other lipids, if necessary, using what I am sending to
>>>>>> you as a template.
>>>>>>
>>>>>> Best,
>>>>>>
>>>>>> Anton.
>>>>>>
>>>>>>
>>>>>> <dopc.cgc>
>>>>>>
>>>>>> <lipid.cgc>
>>>>>>
>>>>>>
>>>>>> On 23 Nov 2008, at 23:56, BIN ZHANG wrote:
>>>>>>
>>>>>>> Hi, all:
>>>>>>> Am I correct that VMD only provide the beads definition for
>>>>>>> protein and water in the CG plugin? Is there any special
>>>>>>> reason for not providing the file for lipid? If anyone can
>>>>>>> give me some reference files of lipid definition, it would be
>>>>>>> great.
>>>>>>> Thanks in advance.
>>>>>>> Bin
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> -------------------------------------------------------------
>>>>>>> The tree of liberty must be refreshed from time to time with
>>>>>>> the blood of patriots and tyrants.
>>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> -------------------------------------------------------------
>>>>> The tree of liberty must be refreshed from time to time with the
>>>>> blood of patriots and tyrants.
>>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> -------------------------------------------------------------
>>> The tree of liberty must be refreshed from time to time with the
>>> blood of patriots and tyrants.
>>
>
>
>
>
>
>
>
>
>
> -------------------------------------------------------------
> The tree of liberty must be refreshed from time to time with the
> blood of patriots and tyrants.

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