[gmx-users] potential energy

[Justin Lemkul]

On 8/11/14, 5:02 AM, Meenakshi Rajput wrote:
> hi users
> i have run energy minimisation of docked complex by using this min.mdp:-
>
> cpp        = /lib/cpp    ; Preprocessor
> include        = -I../top    ; Directories to include in the topology
> format
> integrator    = steep
> emtol        = 1000        ; Stop minimization when the energy changes by
> less than emtol kJ/mol.
> nsteps        = 200        ; Maximum number of (minimization) steps to
> perform
> nstenergy    = 10        ; Write energies to disk every nstenergy steps
> nstxtcout    = 10        ; Write coordinates to disk every nstxtcout steps
> xtc_grps    = Protein    ; Which coordinate group(s) to write to disk
> energygrps    = Protein    ; Which energy group(s) to write to disk
> nstlist        = 5        ; Frequency to update the neighbor list and long
> range forces
> ns_type        = grid      ; Method to determine neighbor list (simple,
> grid)
> rlist        = 1.2        ; Cut-off for making neighbor list (short range
> forces)
> coulombtype    = PME       ; Treatment of long range electrostatic
> interactions
> rcoulomb    = 1.2        ; long range electrostatic cut-off
> rvdw        = 1.2        ; long range Van der Waals cut-off
> constraints    = none        ; Bond types to replace by constraints
> pbc        = xyz        ; Periodic Boundary Conditions (yes/no0
> After the run, potential energy is negative. can you tell me whats the
> problem??
>

There is none.  The potential should be negative.

-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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