VMD-L Mailing List

From: Anton Arkhipov (anton_at_ks.uiuc.edu)
Date: Mon Nov 24 2008 - 18:36:23 CST

Hi Bin,

Yes, you are right, making a residue-based CG model for a large number
of water molecules can be a pain. Indeed, if you have thousands of
water molecules and try to run the CG Builder on such a system, the
memory may become insufficient or at least this will take very long
time.

What you want to do is to avoid coarse-graining your water molecules
directly and instead solvate your CG system (say, protein and lipids)
using CG water. To do this, one just need to create a well-
equilibrated box of CG water, and use it instead of a box of all-atom
water in the solvate plugin of VMD.

Again, I'll send you files for doing this in a separate letter.

Best,

Anton.

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