[gmx-users] In vacuo MD

[Linus Johannissen]

I'm trying to run an in vacuo MD simulation using infinite non-bonding cutoffs, but Gromacs doesn't seem to be calculating the non-bonding interactions - the protein unfolds very rapidly and in the log file the LJ (SR) and Coulomb (SR) values are 0. Does it look like there's something wrong with my mdp file (below), or is it likely to be something else?

Thanks for your help
Linus

mdp file:

title       =  Gas-phase protein simulation
; Run parameters
integrator  = md        ; leap-frog integrator
nsteps      = 50000    ; 2 * 50000 = 100 ps
dt          = 0.001    ; 1 fs
; Output control
nstxout     = 0         ; suppress .trr output
nstvout     = 0         ; suppress .trr output
nstenergy   = 1000      ; save energies every 1 ps
nstlog      = 1000      ; update log file every 1 ps
nstxtcout   = 5000      ; write .xtc trajectory every 5 ps
energygrps  = Protein
; Bond parameters
continuation    = no           ; first dynamics run
constraint_algorithm = lincs    ; holonomic constraints
constraints     = hbonds     ; H-bonds constrained
lincs_iter      = 2             ; accuracy of LINCS
lincs_order     = 4             ; also related to accuracy

comm-mode = angular

; OPTIONS FOR ELECTROSTATICS AND VDW
cutoff-scheme = group
vdw-type    = Cutoff
nstlist     = 0
ns_type     = simple
pbc         = no
rlist       = 0
coulombtype              = cutoff
rcoulomb-switch          = 0
rcoulomb                 = 0
rvdw                     = 0
rvdw-switch              = 0

; Temperature coupling
tcoupl      = v-rescale                     ; modified Berendsen thermostat
tc-grps     = Protein
tau_t       = 0.1                          ; time constant, in ps
ref_t       = 300                            ; reference temperature
; Pressure coupling
pcoupl      = no        ; no pressure coupling in NVT
; Dispersion correction
; Velocity generation
gen_vel     = yes       ; assign velocities from Maxwell distribution
gen_temp    = 300       ; temperature for Maxwell distribution
gen_seed    = -1        ; generate a random seed


___________________
Dr Linus Johannissen
Computational Chemistry Experimental Officer
Manchester Institute of Biotechnology
University of Manchester
UK