From: BIN ZHANG (zhngbn_at_gmail.com)
Date: Mon Nov 24 2008 - 18:24:35 CST

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.