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

[Justin A. Lemkul]

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.

-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

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