[gmx-users] Regarding em potential energy coming possitive

[Justin Lemkul]

On 9/28/16 8:50 PM, Swagata Patra wrote:
> Hello everyone,
>
> I am facing a problem in energy minimization step. I am not sure if the
> system is energy minimized or not. After completing the em, I am getting
> the following message:
> Reached the maximum number of steps before reaching Fmax < 1
>
> Steepest Descents did not converge to Fmax < 1 in 100001 steps.
> Potential Energy  = -9.38185842721980e+06
> Maximum force     =  4.73530543550372e+02 on atom 1694
> Norm of force     =  1.11096437377417e+00
> But when I am calculating the potential energy getting the following
> message:
> Energy                      Average   Err.Est.       RMSD  Tot-Drift
> -------------------------------------------------------------------------------
> Potential                   121.811    1.9e+06        nan   -2017.89
>  (kJ/mol)
>
> Potential energy should come negative. But here its too high.
> One more thing that I want to tell is, in my protein pdb file there is gap
> between amino acids(like G229 then H412). That's why in topology file I am
> getting two chains.
> Please suggest me what could be the problem?
>

I don't see a problem.  The energy is fine and the maximum force is fine for 
most purposes.  You only need to achieve Fmax < 1 for NMA, but to do so you 
probably need a few rounds of EM, not just a single run of steepest descents.

-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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