GROMACS version:2021

GROMACS modification: Yes/No yes

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Dear All

I have added a new residue in a local directory of forcefield. I want to verify the ligand topology for which I am trying to run a minimization in a vacuum. For Simulation in Vacuum, it should be nopbc, no-cutoff and PME with nstlist=0. However with cutoff scheme=Verlet nopbc does not work. So I use a large box size of 100nm with following input parameters:-

; 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 = 10.0 ; 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

nstxout = 100

; 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

cutoff-scheme = Verlet; Buffered neighbor searching

ns_type = simple ; Method to determine neighbor list (simple, grid)

coulombtype = cutoff; Treatment of long-range electrostatic interactions

rcoulomb = 0.001 ; Short-range electrostatic cut-off

rvdw = 0.001 ; Short-range Van der Waals cut-off

constraints = none ; Bond types to replace by constraints

pbc = xyz ; Periodic Boundary Conditions in all 3 dimensions

rlist =0.001 ; Short range neighbour list cutoff

However, I get the value of LJ-14 and Coulomb-14 in output file.

Tolerance (Fmax) = 1.00000e+01

Number of steps = 50000

Step Time

0 0.00000

Energies (kJ/mol)

Bond Angle Proper Dih. LJ-14 Coulomb-14

3.06426e+02 2.25654e+02 2.65055e+02 1.87424e+02 -2.24481e+03

LJ (SR) Coulomb (SR) Potential Pressure (bar)

0.00000e+00 -1.52038e+06 -1.52164e+06 5.25943e-03

How Can I set these to zero so that I can verify the value of any angle or dihedral?

Regards

Sadaf