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

[lina]

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.

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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-- 
Best Regards,

lina