Remove Coulomb interaction

User discussions
1

GROMACS version: 2018
GROMACS modification: No
I am trying to have this instuctions to prevent forming globules of polymer chain.
NO coulomb interaction
LJ cutoff set to 0.3 nm
All-bonds constrained using SHAKE

Gromacs implementation:
constraint_algorithm = shake ; holonomic constraints
constraints = all-bonds ;

; Nonbonded settings
cutoff-scheme = Verlet ; Buffered neighbor searching
ns_type = grid ; search neighboring grid cells
nstlist = 10 ; 20 fs, largely irrelevant with Verlet
rlist = 0.3 ; Short-range cutoff for neighbor list
rvdw = 0.3 ; Short-range van der Waals cutoff (in nm)

DispCorr = EnerPres ; account for cut-off vdW scheme

; Electrostatics
coulombtype = Cutoff ; Turn off Coulomb interactions
rcoulomb = 0.0 ; No electrostatic interactions

Getting error: With Verlet lists rcoulomb!=rvdw is not supported (except for
rcoulomb>rvdw with PME electrostatics)

What’s the best way to do it, without changing the topology file as i want to turn on the coulombic interaction later on.

2

The correct way to do this is to set the charges on all atoms to 0. If you want to make this reversible, then use a user-defined variable in your MDP file, for example

define = -DZEROCHARGE

Then in your topology file(s) you could use an ifdef statement

#ifdef ZEROCHARGE
[ atoms ]
<define atoms with zero charge here>
#else
[ atoms ]
<define atoms with normal charge here>
#endif
1 Like
3

Do I also need to redefine the residue in the .atp file? I added the #ifdef statement in the OPLS-AA non-bonded section, but when running gmx pdb2gmx or performing minimization, the define function is not executing correctly.

Is there a way to implement the WCA potential in GROMACS, similar to how the “shift” command is used in LAMMPS?