[gmx-users] How to examine the problem of one atom during EM
lina.lastname at gmail.com
Wed Jul 27 14:20:01 CEST 2011
On Wed, Jul 27, 2011 at 7:29 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
> lina wrote:
>> 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.
>> Step=42296, Dmax= 2.9e-10 nm, Epot= -2.17267e+05 Fmax= 1.49514e+04, atom=
>> Step=42313, Dmax= 2.0e-10 nm, Epot= -2.17267e+05 Fmax= 2.23506e+04, atom=
>> Step=50000, Dmax= 1.7e-10 nm, Epot= -2.17267e+05 Fmax= 2.89751e+04, atom=
>> 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
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