Fwd: [gmx-users] Editing of the existing system

[James Starlight]

Justin,

Sorry again for the delay.

I've finished minimise my system with the CG algorithm in double precision
( after steep minimisation )
but the output was

Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax < 0.1

Than I've tried to equilibrate this system with the NVT conditions and
obtain old error about collapse of my system :)

 I've found logs of both minimisation ( both of the logs  were very big
I've coppied only end part of those output data )  and attach it to this
topic.

Also I've run minimisation in vacuum as you've told me but this results
would be aviable tomorrow.

Could you tell me whats exactly wrong with that system and is there
possible ways to fix the problem?

Thanks for help


James

31 марта 2012 г. 22:05 пользователь James Starlight
<jmsstarlight at gmail.com>написал:

Justin,
>
> Sorry that I can't provide you with such information now because that data
> have been left in my lab workstation. Tomorrow I'll find all this logs and
> attach it to this topic. Also I've run more properly CG minimisation (
> EMtool=0.01) in double precission mode. I'll check this results too and
> attach all logs here.
>
>
> Many thanks again for help
>
> James
>
> 31 марта 2012 г. 21:57 пользователь Justin A. Lemkul <jalemkul at vt.edu>написал:
>
>
>>
>> James Starlight wrote:
>>
>>> Justin,
>>>
>>> 31 марта 2012 г. 18:18 пользователь Justin A. Lemkul <jalemkul at vt.edu<mailto:
>>> jalemkul at vt.edu>> написал:
>>>
>>>
>>>
>>>    Start by inspecting the initial configuration in the vicinity of
>>>    these atoms. Something is likely clashing here.
>>>
>>>
>>> Yes, I've checked both of the proteins and found that the problem atoms
>>> were situated exactly in the docked region of the both proteins. So It
>>> seems that there are some clashes between atoms in the docked site. By the
>>> way this site of the first protein ( Receptor) consist of 2 flexible loops
>>> and the rigid helix from the second protein. ( fragment of G-protein) Might
>>> the energy minimisation solve this problem generally ? ( e.g by means of CG
>>> minimisation to very low forces aplied on atoms). Is there any possible
>>> ways to change conformation of the flexible loops during minimisation\
>>> equilibration phases without aplication of any external forces?
>>>
>>>
>> Proper EM should resolve such clashes, but under normal circumstances
>> that should have happened already.  You may have to do EM in vacuo before
>> adding any solvent to allow for proper resolution of clashes.  I'm only
>> guessing at this point.  I have asked twice for the output of your previous
>> EM attempts, which would give me a much better idea of where things stand.
>>  Since you haven't answered those questions, I'll leave it up to you to try
>> to resolve.  Good luck.
>>
>> -Justin
>>
>>
>> --
>> ==============================**==========
>>
>> Justin A. Lemkul
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> MILES-IGERT Trainee
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>>
>> ==============================**==========
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