[gmx-users] How to examine the problem of one atom during EM
Justin A. Lemkul
jalemkul at vt.edu
Wed Jul 27 15:06:15 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.
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.
>>> 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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Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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