Re: vmd-l: CG bead definition

From: BIN ZHANG (zhngbn_at_gmail.com)
Date: Tue Nov 25 2008 - 15:01:37 CST

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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