GROMACS version: 2018-2021
GROMACS modification: No
Dear all,
When having a large epsilon and sigma value (eps > 10, sigma > 2.0 nm) the distance where the potential is not repulsive any more is increased. A pbc molecule (a uniform polymer block in vacuum crosslinked through pbc) needs to be at least 4xsigma away from a “wall” (a frozen uniform block of beds in vacuum) to not lead to a too high potential in mdrun’s first step.
What also happens is, that the potential is not attractive anymore. I tested this by pulling the polymer block towards the surface, and the LJ potential is never getting negative.
I am using normal vdw treatment, md integrator in NVT. Periodic only in xy. Using a 12-6 LJ wall at z=0 and z=zmax which has sig,eps=0.0. Very basic setup, tested very different setups too. changed the cutoff, cutoff modifier, rlist, verlet-buffer.
What am I missing? How can this setup lead to a repulsive potential, where the LJ energies never go below zero?
The forcefield.itp is:
[ defaults ]
; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
1 2 no 1.0 1.0
[ atomtypes ]
;name at.num mass charge ptype eps sig
P 1 0.0 0.000 A 10.0 2.0
W 1 0.0 0.000 A 10.0 2.0
[ nonbond_params ]
P W 1 10.0 2.0
[ moleculetype ]
; Name nrexcl
Surface 0
[ atoms ]
1 W 1 W W 1 0.0 10000.0
2 W 1 W W 1 0.0 10000.0
.
.
[ moleculetype ]
; Name nrexcl
Surface 3
[ atoms ]
1 P 1 P P 1 0.0 10000.0
2 P 1 P P 1 0.0 10000.0