[gmx-users] Fwd: Help with Gromacs 5.1 mdp options for CHARMM27 force field

[Rakesh Ramachandran]

Dear all,

     I am using Gromacs 5.1 with CHARMM27 force field for protein
simulation and using the following mdp options. I am really confused
whether to use PME-switch option or only PME and what is the basic
difference. Moreover for CHARMM I see switching needs to be performed, but
with Verlet cutoff should I use Potential-switch, Force-switch
or potential-shift-verlet. Also let me know if any other options need to be
changed.


; NEIGHBORSEARCHING PARAMETERS
; nblist update frequency
nstlist = 40

; ns algorithm (simple or grid)
ns_type = grid ; search neighboring grid cells

; Periodic boundary conditions: xyz, no, xy
pbc                 = xyz ; 3-D PBC

; nblist cut-off
; NBOND CUTNB  (see notes on ELEC below)
;rlist               = 1.4 ; Cut-off for making neighbor list (short range
forces). This is ignored in GPU

; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
; From the CHARMM docs (ewald.doc):
; NBOND EWALD PMEWald KAPPa 0.34 ORDEr 6 CTOFNB 12.0 CUTNB 14.0
coulombtype         = PME-switch ; Treatment of long range electrostatic
interactions
rcoulomb             = 1.2 ; long range electrostatic cut-off

; Relative dielectric constant for the medium and the reaction field
epsilon_r           = 1
epsilon_rf           = 1

; Method for doing Van der Waals
; NBOND VATOM VSWI CTONNB 10.0 CTOFNB 12.0 CUTNB 14.0
cutoff-scheme     = Verlet
vdw-type                = Cut-off
vdw-modifier = Potential-switch

; cut-off lengths
rvdw-switch         = 1.0
rvdw                 = 1.2

; Apply long range dispersion corrections for Energy and Pressure
; NBOND LRC
DispCorr             = EnerPres ; account for cut-off vdW scheme

; Seperate tables between energy group pairs
energygrp_table         =

; Spacing for the PME/PPPM FFT grid
; CHARMM: EWALD recommended spacing: 0.8 A - 1.2 A and 6th Order spline
fourierspacing       = 0.12

; EWALD/PME/PPPM parameters
; (possibly increase pme_order to 6 to match the CHARMM recommendation)
pme_order           = 4
ewald_rtol           = 1e-05
ewald_geometry       = 3d
epsilon_surface     = 0

; OPTIONS FOR WEAK COUPLING ALGORITHMS
; Temperature coupling
Tcoupl               = V-rescale ; modified Berendsen thermostat
tau_t               = 0.1 0.1 ; time constant, in ps
tc-grps             = Protein non-Protein ; two coupling groups - more
accurate
ref_t               = 300 300 ; reference temperature, one for each group,
in K

; Pressure coupling
Pcoupl               = Parrinello-Rahman ; Pressure coupling on in NPT
Pcoupltype           = isotropic ; uniform scaling of box vectors

; Time constant (ps), compressibility (1/bar) and reference P (bar)
tau_p               = 2.5 ; time constant, in ps
compressibility     = 4.5e-5 ; isothermal compressibility of water, bar^-1
ref_p               = 1.0 ; reference pressure, in bar

; OPTIONS FOR BONDS
; CHARMM uses SHAKE with tol 1e-6
constraints   = h-bonds   ; Constrain hydrogen bonds
constraint_algorithm = LINCS     ; Type of constraint algorithm
continuation   = yes       ; Do not constrain the start configuration
(yes/no)
lincs_iter = 1 ; accuracy of LINCS
shake_tol             = 0.0001   ; Relative tolerance of shake
lincs_order         = 4         ; Highest order in the expansion of the
constraint coupling matrix
lincs_warnangle       = 30       ; Rotate over more degrees than

; Velocity generation
;
gen_vel = no ; Velocity generation is off

; the output
;
nstxout       = 2500             ; Frequency to write coordinates to output
trajectory file, save coordinates every 5 ps
nstvout       = 2500             ; Frequency to write velocities to output
trajectory file, save velocities every 5 ps

; Output frequency for energies to log file and energy file
nstlog       = 2500             ; Frequency to write energies to log file,
update log file every 5 ps
nstenergy   = 2500             ; Frequency to write energies to energy
file, save energies every 5 ps

; Output frequency and precision for xtc file
nstxout-compressed     = 2500               ; Frequency to write
coordinates to xtc trajectory, xtc compressed trajectory every 5 ps
compressed-x-grps     = System           ; Group(s) to write to xtc
trajectory
energygrps   = System ; Group(s) to write to energy file

comm_mode               = Linear              ; remove center of mass
translation
nstcomm                 = 1000                ; [steps] frequency of mass
motion removal
comm_grps               = System    ; group(s) for center of mass motion
removal