[gmx-users] energy group exclusion in gromacs 5.0.2

[Steven Neumann]

Dear Gmx Users,

I wish to compare simulation of peptides in water with and without excluded
non-bonded parameters. My mdp file without exclusions:

; Run parameters
integrator  = md        ; leap-frog integrator
nsteps      = 50000000    ; 100 ns
dt          = 0.002     ; 2 fs
; Output control
nstxout     = 0     ; suppress .trr output ; output coordinates every 25 ps
nstvout     = 0     ; velocities to output every 25000 steps
nstenergy   = 1000      ; save energies every 2 ps
nstlog      = 1000      ; update log file every 2 ps
nstxtcout   = 5000         ; suppress (tlumic) xtc trajectory
continuation    = yes           ; first dynamics run
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
cutoff-scheme    = Verlet
ns_type     = grid      ; search neighboring grid cells
nstlist     = 20         ; 10 fs
vdwtype     = cut-off
rvdw-switch = 1.0
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)
ewald_rtol  = 1e-5      ; relative strenght of the Ewald-shifted potential
rcoulomb
; Electrostatics
coulombtype     = PME       ; Particle Mesh Ewald for long-range
electrostatics
pme_order       = 4         ; cubic interpolation
fourierspacing  = 0.12      ; grid spacing for FFT
coulomb-modifier         = Potential-shift
; Temperature coupling is on
tcoupl      = V-rescale                     ; modified Berendsen thermostat
tc_grps     = Protein Water        ; two coupling groups - more accurate
tau_t       = 0.1 0.1                    ; time constant, in ps
ref_t       = 308 308                    ; reference temperature, one for
each group, in K
; Pressure coupling is on
pcoupl      = Parrinello-Rahman             ; pressure coupling is on for
NPT
pcoupltype  = isotropic                     ; uniform scaling of box vectors
tau_p       = 2.0                           ; time constant, in ps
ref_p       = 1.0                           ; reference pressure, in bar
compressibility = 4.5e-5                    ; isothermal compressibility of
water, 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       ; assign velocities from Maxwell distribution

so i wish to include

energygrps = Protein
energygrp_excl = Protein Protein


So i need to also change

cutoff-scheme    = group

Then I get errors and notes:

NOTE 1 [file md_excl.mdp]:
  The group cutoff scheme is deprecated in Gromacs 5.0 and will be removed
  in a future release when all interaction forms are supported for the
  verlet scheme. The verlet scheme already scales better, and it is
  compatible with GPUs and other accelerators.


NOTE 2 [file md_excl.mdp]:
  With exact cut-offs, rlist should be larger than rcoulomb and rvdw, so
  that there is a buffer region for particle motion between neighborsearch
  steps


NOTE 3 [file md_excl.mdp]:
  For energy conservation with switch/shift potentials, rlist should be 0.1
  to 0.3 nm larger than rcoulomb.

WARNING 1 [file md_excl.mdp]:
  Can not exclude the lattice Coulomb energy between energy groups


Istn it better for to have vdwtype = Switch/Shift in the group scheme?
What are the best settings for energy exclusions in Gmx 5? Can someone
provide example mdp?

thanks,

Steven