Re: CG bead definition

From: BIN ZHANG (zhngbn_at_gmail.com)
Date: Thu Oct 22 2009 - 18:05:32 CDT

Dear Valeria:

It would be good to keep the mail on the list so that other
experienced users can also help you. ;-)

To really pin down your problem, more info is needed here, like what
parameters you are using in the config file, and what error are you
getting?

In the mean time, you can take a look at the attached config file,
which was originally sent to me by Anton.

Hope this helps.
Best,
Bin

On Oct 22, 2009, at 7:48 AM, Valeria Marquez wrote:

> Thanks Bin for your answer. Previously I was using 2.4 boundary for
> water box. I'm trying now with 5.0 boundary, but later a 1000 steps
> of minimization, the system seems frozen and it doesn't move
> anymore. The simulation stops at 5 ps of MD. What is going on? The
> temperature of simulation is 323 K. Should I get the temperature
> high?
>
> Thanks a lot,
>
> Valeria Marquez.
>
> 2009/10/20 BIN ZHANG <zhngbn_at_gmail.com>
> 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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