[gmx-users] using charmm36 force field with gromacs

[Yoav Atsmon-Raz]

Hi there,

I'm a noob with Gromacs 4.6.7 which is interested in doing all-atom simulations with the charmm36 force field for a protein-membrane system while applying the Verlet cutoff  scheme. Basically I have two questions regarding this matter:
1) Does using the CHARMM36 ff necessitates any special modifications to the mdp files (minimization,equilibration,prod. run)?
2) Besides the "cutoff-scheme=verlet" line in the mdp files, do I need to add anything else?

This is my prod. run mdp file:

; Run parameters
integrator    = md        ; leap-frog integrator
nsteps        = 50        ; 2 * 500000 = 1000 ps (1 ns)
dt            = 0.002        ; 2 fs
; Output control
nstxout        = 10        ; save coordinates every 2 ps
nstvout        = 10        ; save velocities every 2 ps
nstxtcout    = 10        ; xtc compressed trajectory output every 2 ps
nstenergy    = 10    ; save energies every 2 ps
nstlog        = 10        ; update log file every 2 ps
; Bond parameters
continuation    = yes            ; Restarting after NPT
constraint_algorithm = lincs    ; holonomic constraints
constraints    = all-bonds            ; all bonds (even heavy atom-H bonds) constrained
lincs_iter    = 1                    ; accuracy of LINCS
lincs_order    = 4                    ; also related to accuracy
; Neighborsearching
ns_type        = grid        ; search neighboring grid cels
nstlist        = 5            ; 10 fs
rlist        = 1.2        ; short-range neighborlist cutoff (in nm)
rcoulomb    = 1.2        ; short-range electrostatic cutoff (in nm)
rvdw        = 1.2        ; short-range van der Waals cutoff (in nm)
cutoff-scheme   = Verlet
; Electrostatics
coulombtype    = PME        ; Particle Mesh Ewald for long-range electrostatics
pme_order    = 4            ; cubic interpolation
fourierspacing    = 0.16        ; grid spacing for FFT
; Temperature coupling is on
tcoupl        = Nose-Hoover            ; More accurate thermostat
tc-grps        = POPC_Protein Water            ; two coupling groups - more accurate
tau_t        = 0.5    0.5                ; time constant, in ps
ref_t        = 323     323                ; reference temperature, one for each group, in K
; Pressure coupling is on
pcoupl        = Parrinello-Rahman        ; Pressure coupling on in NPT
pcoupltype    = semiisotropic            ; uniform scaling of x-y box vectors, independent z
tau_p        = 2.0                    ; time constant, in ps
ref_p        = 1.0    1.0                ; reference pressure, x-y, z (in bar)
compressibility = 4.5e-5    4.5e-5    ; isothermal compressibility, bar^-1
; Periodic boundary conditions
pbc            = xyz        ; 3-D PBC
; Dispersion correction
DispCorr    = EnerPres    ; account for cut-off vdW scheme
; Velocity generation
gen_vel        = no        ; Velocity generation is off
; COM motion removal
; These options remove motion of the protein/bilayer relative to the solvent/ions
nstcomm         = 1
comm-mode       = Linear
comm-grps       = POPC_Protein Water


Thanks in advance to anyone answering this!