Changing nstlist/rlist in gmx mdrun- Charmm36 forcefield

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1

GROMACS version: Gromacs 2020.3 or 2021.3
GROMACS modification: No

New to MD- Have lots to learn! I have noticed in my md runs, using the charmm36 forcefield, my nstlist and therefore rlist values are being changed due to nstlist tuning. I understand that nstlist is a minimum value and mdrun can increase it. However I was wondering what this means for my simulations since rlist is being increased from 1.2, which I believe is what it should be set at for charmm36.

mg.log output- “Changing nstlist from 10 to 80, rlist from 1.2 to 1.32”

mdp file parameters

; Run parameters
integrator = md ;
nsteps = 500000 ;
dt = 0.002 ;

; Output control
nstxout = 0 ; save coordinates every 2 ps
nstvout = 0 ; save velocities every 2 ps
nstfout = 0
nstxout-compressed = 5000 ; xtc compressed trajectory output every 10 ps
nstenergy = 5000 ; save energies every 10 ps
nstlog = 5000 ; update log file every 10 ps
compressed-x-grps = System

; Bond parameters
continuation = yes ; Restarting after NPT
constraint_algorithm = lincs ; holonomic constraints
constraints = h-bonds ; all bonds (even heavy atom-H bonds) constrained
lincs_iter = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy

; Neighborsearching
cutoff-scheme = Verlet
ns_type = Grid ;
nstlist = 10 ;
rlist = 1.2 ;
vdwtype = Cut-off
vdw-modifier = Force-switch
rvdw_switch = 1.0
rvdw = 1.2 ;
rcoulomb = 1.2 ;

; Electrostatics
coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics
pme_order = 4 ; cubic interpolation
fourierspacing = 0.135 ; grid spacing for FFT

; Temperature coupling is on
tcoupl = v-rescale ;
tc-grps = Protein Water_and_ions ;
tau_t = 0.2 0.2 ;
ref_t = 310 310 ;

; Pressure coupling is on
pcoupl = Parrinello-Rahman ;
pcoupltype = isotropic ;
tau_p = 2.0 ;
ref_p = 1.0 ;
compressibility = 4.5e-5 ;

; Periodic boundary conditions
pbc = xyz ; 3-D PBC

; Dispersion correction
DispCorr = no ; account for cut-off vdW scheme off in charmm36
; Velocity generation
gen_vel = no ; velocity generation off
gen_temp = 310
gen_seed = -1

; COM motion removal
;
nstcomm = 100
comm-mode = Linear
comm-grps = Protein Water_and_ions

; Scale COM of reference coordinates
refcoord_scaling = com

2

Tuning of the value is fine, because a buffered list is expected to be used. In practice, we actually use longer values in e.g. CHARMM and NAMD (14-16 Å) simply for bookkeeping purposes. GROMACS does this automatically and finds the appropriate value. Setting rlist = 1.2 is appropriate since the neighborlist cutoff should never be shorter than the longest nonbonded cutoff (for CHARMM, this is the tail end of the switching range for LJ).

3

Hi,

The force field only requires the LJ cutoff to be 1.2 nm, not a specific list cutoff (rlist) which is a free parameter in GROMACS as we use an algorithm which allows accuracy-based calculation of rlist for a given tolerance verlet-buffer-tolerance.

To learn more check out the manual section on this:

Cheers,
Szilárd