# Changing nstlist/rlist in gmx mdrun- Charmm36 forcefield **URL:** \ **Category:** User discussions\ **Tags:** forcefield, mdp-parameters, mdrun, simulation-setup\ **Created:** [June 14, 2022, 1:11pm UTC](https://gromacs.bioexcel.eu/t/changing-nstlist-rlist-in-gmx-mdrun-charmm36-forcefield/4294 "2022-06-14T13:11:25Z")\ **Posts on this page:** 3\ **Page:** 1
**Author:** ![STx19](https://avatars.discourse-cdn.com/v4/letter/s/edb3f5/32.png) [@STx19](https://gromacs.bioexcel.eu/u/STx19)\ **Post date:** [June 14, 2022, 1:11pm UTC](https://gromacs.bioexcel.eu/t/changing-nstlist-rlist-in-gmx-mdrun-charmm36-forcefield/4294/1 "2022-06-14T13:11:25Z")
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 ---
**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\ **Post date:** [June 14, 2022, 6:52pm UTC](https://gromacs.bioexcel.eu/t/changing-nstlist-rlist-in-gmx-mdrun-charmm36-forcefield/4294/2 "2022-06-14T18:52:44Z")
> [@STx19](#): > > 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. 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). ---
**Author:** ![pszilard](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/pszilard/32/21_2.png) [@pszilard](https://gromacs.bioexcel.eu/u/pszilard)\ **Post date:** [June 14, 2022, 6:55pm UTC](https://gromacs.bioexcel.eu/t/changing-nstlist-rlist-in-gmx-mdrun-charmm36-forcefield/4294/3 "2022-06-14T18:55:32Z")
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: - [Molecular Dynamics — GROMACS 2022 documentation](https://manual.gromacs.org/2022/reference-manual/algorithms/molecular-dynamics.html#pair-lists-generation) - and the related mdp parameter documentation: [Molecular dynamics parameters (.mdp options) — GROMACS 2022 documentation](https://manual.gromacs.org/documentation/2022/user-guide/mdp-options.html#neighbor-searching) Cheers, Szilárd