[gmx-users] Cutoff settings for CHARMM36

Siew Wen Leong ariel.leongsw at gmail.com
Tue Mar 6 10:28:32 CET 2012

Dear Gromacs users,

Below is part of my mdp file for a membrane protein simulation with
CHARMM36. May I know what is the recommended value for rlist? I have gone
through Klauda's paper and some threads in the user list, particularly
http://www.mail-archive.com/gmx-users@gromacs.org/msg34582.html but could
not determine a good rlist value. Grompp and the manual noted that rlist
should be larger than rvdw for switch/shift function by 0.1-0.3nm to
account for size of charge group and diffusion between neighbour list
updates. What is the effect of ignoring this note and will this result in
incorrect energy values?

; Neighborsearching parameters
ns_type   = grid                    ; search neighboring grid cels
rlist         = 1.2                       ; short-range neighborlist cutoff
(in nm)
rcoulomb = 1.2                       ; short-range electrostatic cutoff (in
rvdw       = 1.2                       ; short-range van der Waals cutoff
(in nm)
rlistlong  = 1.4                       ; long-range neighbourlist cutoff
(in nm)

; Van der Waals (LJ)
vdwtype          = switch    ; switch potential for LJ terms
rvdw_switch    = 0.8        ; start switching LJ potential

; Electrostatics
coulombtype    = PME        ; Particle Mesh Ewald for long-range
pme_order       = 4              ; cubic interpolation
fourierspacing  = 0.16        ; grid spacing for FFT

DispCorr    = no        ; account for cut-off vdW scheme, none as per C36
Leong Siew Wen

“Making the simple complicated is commonplace; making the complicated
simple, awesomely simple, that’s creativity.”
 *- Charles Mingus-*
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