[gmx-users] How to examine the problem of one atom during EM

[Justin A. Lemkul]

lina wrote:
> On Wed, Jul 27, 2011 at 9:06 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>>
>> lina wrote:
>>> On Wed, Jul 27, 2011 at 7:29 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>>>> lina wrote:
>>>>> Hi,
>>>>>
>>>>> Form the begining to 50000 steps, during EM, all exit in atom 8524,
>>>>> how do I check it further? I mean, from which parts to examine?
>>>>> I also switched to double version to run the EM.
>>>>>
>>>> Open your structure in a visualization program and look at what it might
>>>> be
>>>> clashing with
>>> Thanks, I checked before.
>>>
>> And what did you find?  What is the closest atom to the one with the maximal
>> force?  Would its charge cause repulsion?  Is it so close that LJ overlap is
>> causing a problem?  In this case, visualization of the problematic structure
>> is the solution, you just have to take care to identify the source of the
>> problem.  It certainly may not always be obvious.
> 
> Thanks, I guess I might make the system so compact.
> 
> Before in VMD it showed something weird, kind of broken bond, but in
> PyMOL was fine.
> 

Well, the bond didn't actually break, but that's clearly where the problem is. 
You have some sort of geometric strain.  The EM process should have produced a 
.trr file, which, if you saved coordinates frequently enough, should let you see 
how that strained structure evolved.

-Justin

> Thanks again,
> 
>> -Justin
>>
>>>> -Justin
>>>>
>>>>> ....
>>>>> Step=42296, Dmax= 2.9e-10 nm, Epot= -2.17267e+05 Fmax= 1.49514e+04,
>>>>> atom=
>>>>> 8524
>>>>> ...
>>>>> Step=42313, Dmax= 2.0e-10 nm, Epot= -2.17267e+05 Fmax= 2.23506e+04,
>>>>> atom=
>>>>> 8524
>>>>> ...
>>>>> Step=50000, Dmax= 1.7e-10 nm, Epot= -2.17267e+05 Fmax= 2.89751e+04,
>>>>> atom=
>>>>> 8524
>>>>>
>>>>> writing lowest energy coordinates.
>>>>>
>>>>> Steepest Descents did not converge to Fmax < 1000 in 50001 steps.
>>>>> Potential Energy  = -2.17266924593509e+05
>>>>> Maximum force     =  2.89751132744731e+04 on atom 8524
>>>>> Norm of force     =  2.18622026854678e+02
>>>>>
>>>>> Thanks for any advice,
>>>>>
>>>> --
>>>> ========================================
>>>>
>>>> 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
>>>>
>>>> ========================================
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>>>
>>>
>> --
>> ========================================
>>
>> 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
>>
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> 
> 
> 

-- 
========================================

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

========================================