[gmx-users] Potential Energy is positive on minimizing the system

[Justin Lemkul]

On 2/23/17 8:23 AM, Anurag Dobhal wrote:
> Dear gromacs users,
>
> I am Simulating a polymer chain having 20 monomer units. I am doing the
> simulation in the vaccum (I am not solvating the system). The total charge
> in my polymer chain is +9 and I am not nutrealizing the system as I was
> suggested earlier that if we are  simulating a system in a vaccum we can
> continue without neutralizing the system (https://www.mail-archive.com/
> gromacs.org_gmx-users at maillist.sys.kth.se/msg23520.html).
>
> Now when I am minimizing my system I am not getting negative potential
> energy (Potential Energy  =  4.5656064e+03). I am using gromacs Version
> 4.6.5 and the parameters of the minim.mdp are below
>
> ; minim.mdp - used as input into grompp to generate em.tpr
> ; Parameters describing what to do, when to stop and what to save
> integrator = steep ; Algorithm (steep = steepest descent minimization)
> emtol = 1000.0   ; Stop minimization when the maximum force < 1000.0
> kJ/mol/nm
> emstep          = 0.01          ; Energy step size
> nsteps = 50000    ; Maximum number of (minimization) steps to perform
>
> ; Parameters describing how to find the neighbors of each atom and how to
> calculate the interactions
> nstlist = 1 ; Frequency to update the neighbor list and long range forces
> ns_type = grid ; Method to determine neighbor list (simple, grid)
> rlist = 1.0 ; Cut-off for making neighbor list (short range forces)
> coulombtype = PME ; Treatment of long range electrostatic interactions
> rcoulomb = 1.0 ; Short-range electrostatic cut-off
> rvdw = 1.0 ; Short-range Van der Waals cut-off
> pbc = xyz  ; Periodic Boundary Conditions (yes/no)
>
>
> Any help will be appreciated. Thank you
>

That's normal.  But your .mdp file is not truly in vacuo since you're using PME 
and PBC.  But you should expect a positive energy when there's no solvent.

-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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