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