Re: CG bead definition

From: BIN ZHANG (zhngbn_at_gmail.com)
Date: Tue Oct 20 2009 - 15:12:04 CDT

Hi, Valeria:

Can I ask how you solvated your system? Did you specify a boundary
parameter to add the water box? If so, one thing to remember is that
now the default should be around 5 rather than 2.4 as in all-atom model.

Hope this helps.
Bin

On Oct 20, 2009, at 1:00 PM, Valeria Marquez wrote:

>
> Dear Bin:
>
> I appreciate your help. I'm been following your suggestions, and I
> built the system as you explain me. But when I run the minimization,
> the simulation stops without a reason. I can see in the output that
> the potential energy is too high. Do you have any ideas about the
> reason of that?
>
> Thank you in advance
>
> Cheers.
>
> Valeria Marquez.
>
> 2009/10/20 BIN ZHANG <zhngbn_at_gmail.com>
> Hi Valeria,
>
> While working with RBCG, it's better to solvate the cg protein with
> coarse-grained water, rather than coarse graining all-atom water.
> This can be done using the scripts provided by Anton, as forwarded
> below.
>
> Best,
> Bin
>
>
> Begin forwarded message:
>
>> From: Anton Arkhipov <anton_at_ks.uiuc.edu>
>> Date: August 31, 2009 9:24:05 PM PDT
>> To: vmd-l_at_ks.uiuc.edu
>> Cc: Yannick Misteli <yannickmisteli_at_berkeley.edu>, wang <c00jsw00_at_nchc.org.tw
>> >
>> Subject: Re: vmd-l: CG bead definition
>>
>> Hi,
>>
>> Because of several questions about the files for RBCG modeling in
>> VMD, I have put some useful files on the web. Please see here:
>>
>> http://www.ks.uiuc.edu/Research/CG/rbcg/files/
>>
>> Best,
>>
>> Anton.
>>
>>
>>
>> On Aug 25, 2009, at 3:02 PM, Yannick Misteli wrote:
>>
>>> Hi Anton,
>>>
>>> I was reading your thread on the vmd/namd mailing list about
>>> cgbuilder and was wondering if you could provide me with the files
>>> as well (dopc.cgc, lipid.cgc ect.)?
>>>
>>> Thanks a lot
>>>
>>> ~yannick
>>>
>>
>>
>>
>> On Aug 26, 2009, at 12:46 AM, wang wrote:
>>> Dear Anton,
>>> Could you sent the two files (lipid.cgc and dopc.cgc) to me?
>>> Thanks
>>>
>>> Y.T Wang
>>>
>>>
>>> <c00jsw00.vcf>
>>>
>
>

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