[gmx-users] About EM for Cyclic Peptide

[Justin Lemkul]

On 9/15/12 10:45 AM, vidhya sankar wrote:
> Dear Mark Thank your excellent and patience Reply.
>
> it is very useful I Did as you Instruct in Gromacs Mailing List
>
> But when I DO Energy Minimization I have got following error
>
> Steepest Descents converged to machine precision in 31 steps,
> but did not reach the requested Fmax < 1000.
> Potential Energy  =                  -nan
> Maximum force     =  1.36683186708214e+07 on atom 26
> Norm of force     =                  -nan
>
> Even I have Adjusted the Various Parameters Namely
>
> emtol and  emstep still the same thing is repeated
>

The outcome suggests there is something catastrophically wrong with the topology 
such that energies are essentially infinite.

-Justin

-- 
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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