[gmx-users] change in energy minimization

[Justin Lemkul]

On 11/10/14 12:16 AM, md kashif wrote:
> Dear all
> I am new user and stuck with the energy minimization conflict.
> I am following the gromacs tutorial (
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/index.html
>   ,lysozyme
> in water) for my protein and getting the energy minimized protein with
> Epot= -1.5248922e+06  is this value correct? I have used mdp files same as
> given in the sample tutorial.

There is no way to know what the "correct" value is for any given system.  If 
the potential is negative and Fmax has converged below emtol, then minimization 
did its job.

-Justin

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

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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