[gmx-users] Help regarding potential energy

[Justin Lemkul]

On 4/26/14, 6:05 AM, Gaurav Saraf IDD M Tech Biochem. Engg, IIT (BHU) wrote:
> Dear Gromacs users,
> I am doing a protein-peptide simulation using gromos43a1 forcefield
> (as per the tutorial)
> When i do the energy minimization step before beginning equilibration,
> I get the following results:
>
> Steepest Descents converged to Fmax < 1000 in 652 steps
> Potential Energy  = -8.04234816499126e+05
> Maximum force     =  9.71976935137859e+02 on atom 4612
> Norm of force     =  2.70955252439520e+01
>
> But when I check with g_energy_d -f em.edr (and then 10 0 {for
> potential}), I get
>
> Energy                      Average   Err.Est.       RMSD  Tot-Drift
> -------------------------------------------------------------------------------
> Potential                1.36118e+09    1.3e+09 1.52478e+10
> -7.91307e+09  (kJ/mol)
>
> The potential is showing positive... what could be wrong?
>

The average potential energy of an energy minimization run is not a useful 
quantity.  Plot the output .xvg file - you'll see very high energies in the 
first few steps, but the energy converges to an acceptable value, as the printed 
information suggests.

-Justin

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

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
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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