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

Anurag Dobhal anurag.dobhal at nano-medicine.co.in
Thu Feb 23 14:19:49 CET 2017

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 (

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
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

*Anurag Dobhal*
*Graduate Student (Bioprocess Technology)*
*Institute of Chemical Technology, Mumbai*



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