[gmx-users] potential energy is from energy mimization

[Justin Lemkul]

On 3/18/15 9:42 PM, Rj wrote:
> Dear gmx,
>
>
> I am simulation a kinase protein which has (~1200 aa) length. When I energy minimize the protein with default em file from Justin A. Lemku tutorial. i have got the following output.
>
>
> writing lowest energy coordinates.
>
>
> Steepest Descents converged to Fmax < 1000 in 1162 steps
> Potential Energy  = -4.6686910e+06
> Maximum force     =  9.6213324e+02 on atom 10673
> Norm of force     =  1.6875889e+01
>
> After i plot the potential and through " gmx energy -f em.edr -o potential.xvg " by selecting potential (15) and 0, i end up with following results..
> Energy                      Average   Err.Est.       RMSD  Tot-Drift
> -------------------------------------------------------------------------------
> Potential                1.97914e+09      2e+09 5.83904e+10 -1.18272e+10  (kJ/mol)
>

The average potential during EM has no use.

>
>
>
> When i try to see this value in xmgrace plot, i ccouldnt see any plot. Doesnt mean my system is not relaxed well? Should i need to increase the steps of em ? if so, how do i ? Thanks.
>

Probably the potential just drops precipitously and the resulting scale is such 
that you can't clearly see it.  Look at the .xvg in a text editor and you will 
see the progression of the energy, or adjust the scale in Grace.

-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

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