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

[Justin A. Lemkul]

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.

-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
>>
>> ========================================
>> --
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> Please don't post (un)subscribe requests to the list. Use the www interface
>> or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
> 
> 
> 

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

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

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