[gmx-users] Potential energy positive

Suman Das sumandas212 at gmail.com
Mon Nov 2 15:24:47 CET 2015

Hi All,
I am simulating molten urea (contains only urea molecule) at 406 K. After
the energy minimization, I found the potential energy positive (~10^4 ).

Steepest Descents converged to Fmax < 100 in 646 steps
Potential Energy  =  3.8694098e+04
Maximum force     =  8.9818977e+01 on atom 26
Norm of force     =  2.2291134e+01

I have used these potential parameters of urea previously for simulating
acetamide+urea  mixtures which gives results matching closely with the
experimental ones. Please see below my input file:
; 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 = 100.0   ; Stop minimization when the maximum force < 50.0 kJ/mol/nm
emstep          = 0.001         ; Energy step size
nsteps = 10000   ; Maximum number of (minimization) steps to perform

; Parameters describing how to find the neighbors of each atom and how to
calculate the interactions
nstlist = 2 ; Frequency to update the neighbor list and long range forces
ns_type = grid ; Method to determine neighbor list (simple, grid)
rlist = 1.3   ; Cut-off for making neighbor list (short range forces)
coulombtype = PME ; Treatment of long range electrostatic interactions
rcoulomb = 1.3 ; Short-range electrostatic cut-off
rvdw = 1.3 ; Short-range Van der Waals cut-off
pbc = xyz ; Periodic Boundary Conditions (yes/no)

Can you suggest me what should I do to overcome the potential energy


Suman Das
Senior Research Fellow,
Dept. of Chemical Biological and Macromolecular Sciences
S.N.Bose National Centre For Basic Sciences,
Block-JD, Sector-III, Salt Lake City
Kolkata-700098, India

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