[gmx-users] membed in mdrun VERSION 5.0.4

[Nash, Anthony]

Hi all,

I thought I would try using the -membed option of mdrun to insert a
helical dimer into a lipid bilayer. I¹ve followed the .mdp instructions on
g_membed to generate my required .tpr file. Upon calling grommp I get:

ERROR 1 [file membed_NPT.mdp]:
  Energy group exclusions are not (yet) implemented for the Verlet scheme


My input file can be seen below. If seems as though the Integrator is the
issue, even though I¹ve picked the correct one. Is a place holder feature?

Many thanks
Anthony

integrator = md
energygrps = Protein
freezegrps = Protein
freezedim = Y Y Y
energygrp_excl = Protein Protein


nsteps          = 5000000       ; 2 * 500000 = 1000 ps (2 ns)
dt                  = 0.002             ; 2 fs
nstxout         = 10000         ; save coordinates every 0.2 ps
nstvout         = 10000         ; save velocities every 0.2 ps
nstenergy       = 10000         ; save energies every 0.2 ps
nstlog          = 10000         ; update log file every 0.2 ps

continuation    = yes               ; Restarting after NVT
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

ns_type         = grid          ; search neighboring grid cels
nstlist         = 5                 ; 10 fs
rlist           = 1.0           ; short-range neighborlist cutoff (in nm)
rcoulomb        = 1.0           ; short-range electrostatic cutoff (in nm)
rvdw            = 1.0           ; short-range van der Waals cutoff (in nm)

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

tcoupl          = Berendsen   ;Nose-Hoover                  ; More
accurate thermostat
tc-grps         = Protein  POPC SOL     ; three coupling groups - more
accurate
tau_t           = 0.5   0.5 0.5                 ; time constant, in ps
ref_t           = 310   310 310                 ; reference temperature,
one for each group, in K

pcoupl          = Parrinello-Rahman         ; Pressure coupling on in NPT
pcoupltype      = semiisotropic             ; uniform scaling of x-y box
vectors, independent z
tau_p           = 5.0                           ; 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

pbc                 = xyz               ; 3-D PBC
DispCorr        = EnerPres      ; account for cut-off vdW scheme
gen_vel         = no            ; Velocity generation is off
nstcomm         = 1
comm-mode       = Linear
comm-grps       = POPC_Protein SOL
refcoord_scaling = com