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

[lina]

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.


>
> -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
>



-- 
Best Regards,

lina