Hexane simulation box

User discussions
1

Hello there,

I’m trying to do a equilibrated hexane box. I have got the topology for gromacs by using the ligand reader and the force field converter in CHARMM-GUI. Then I have created the simulation box by using gmx insert-molecules. I have done the energy minimization using the suggested parameters for charmm ff, but I have a final positive potential energy.
Here the .mdp 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 = 1000.0 ; Stop minimization when the maximum force < 1000.0 kJ/mol/nm
emstep = 0.01 ; Minimization 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 = 10 ; Frequency to update the neighbor list and long range forces
cutoff-scheme = Verlet ; Buffered neighbor searching
vdwtype = cutoff
vdw-modifier = force-switch
rlist = 1.2
rvdw = 1.2 ; Short-range Van der Waals cut-off
rvdw-switch = 1.0
ns_type = grid ; Method to determine neighbor list (simple, grid)
coulombtype = PME ; Treatment of long range electrostatic interactions
rcoulomb = 1.2 ; Short-range electrostatic cut-off
DispCorr = no
pbc = xyz ; Periodic Boundary Conditions in all 3 dimensions

Thank you in advance
Matteo

2

Hi Matteo,

more important than the absolute final potential energy is its behaviour during minimisation - if it’s reducing it’s fine, the expected behaviour is a quite sharp drop in the beginning and then a levelling - out.

3

For weakly interacting species like hydrocarbons, the magnitude of the internal (bonded) terms, which are strictly positive, will almost always overcome any favorable intermolecular interactions. So it is typical to see a positive energy in these systems.