GROMACS version: 2022.3-plumed_2.8.1
GROMACS modification: Yes/No
Hi all,
I am having an assignment to do simple Umbrella Sampling simulation to calculate Free energy profile for martinized (Martini 3) small peptide and simple POPC membrane bilayer. I tried pushing the peptide all teh way through the membrane, but the pmf is very unsymmetrical and I seem to have holes in my windows which I dont know how to fill. Also I find it weird that the peptide doesnt want to adsorb to the membrane at all.
I tried adding more windows and widening them but I still have a hole there.
I was then recomended to run steered simulation on just one side and pull away from one of the sides of the membrane, but trying that I am not able run the sim at all. I mostly encountered this error and have no clue how to fix it
“Fatal error: Domain decomposition has not been implemented for box vectors that have non-zero components in directions that do not use domain decomposition: ncells = 1 1 8, box vector[3] = -nan -nan -nan”
pull.mdp used:
integrator = md
tinit = 0.0
dt = 0.020
nsteps = 2000000
nstxout = 5000
nstvout = 5000
nstfout = 5000
nstlog = 5000
nstenergy = 5000
nstxout-compressed = 5000
compressed-x-precision = 100
cutoff-scheme = Verlet
nstlist = 20
ns_type = grid
pbc = xyz
verlet-buffer-tolerance = 0.005
epsilon_r = 15
coulombtype = reaction-field
rcoulomb = 1.1
vdw_type = cutoff
vdw-modifier = Potential-shift-verlet
rvdw = 1.1
tcoupl = v-rescale
tc-grps = system
tau_t = 1.0
ref_t = 310.15
; Pressure coupling:
Pcoupl = Parrinello-rahman
Pcoupltype = semiisotropic
tau_p = 12.0
compressibility = 3e-4 3e-4
ref_p = 1.0 1.0
; GENERATE VELOCITIES FOR STARTUP RUN:
gen_vel = no
refcoord_scaling = com
; COM pulling
pull = yes
pull-nstxout = 1000
pull-nstfout = 1000
pull-ngroups = 2
pull-group1-name = POPC
pull-group2-name = Protein
pull-ncoords = 1
pull-coord1-type = umbrella
pull-coord1-geometry = cylinder
pull-cylinder-r = 1.5
pull-coord1-groups = 1 2
pull-coord1-dim = N N Y
pull-coord1-vec = 0 0 -1
pull-coord1-start = yes ; Start from initial distance
pull-coord1-init = 0
pull-coord1-rate = 0.0001 ; Pulling rate in nm/ps
pull-coord1-k = 1000 ; Spring constant in kJ/mol/nm^2
us.mdp used:
define =
integrator = md
tinit = 0.0
dt = 0.02
nsteps = 25000000
comm-mode = Linear
nstcomm = 100
comm-grps = system
nstlog = 10000
nstenergy = 1000
nstxout-compressed = 10000
compressed-x-precision = 1000
cutoff-scheme = Verlet
nstlist = 20
ns_type = grid
pbc = xyz
verlet-buffer-tolerance = 0.005
epsilon_r = 15
coulombtype = reaction-field
rcoulomb = 1.1
vdw_type = cutoff
vdw-modifier = Potential-shift-verlet
rvdw = 1.1
tcoupl = v-rescale
tc-grps = system
tau_t = 1.0
ref_t = 310.15
; Pressure coupling:
Pcoupl = Parrinello-Rahman
Pcoupltype = semiisotropic
tau_p = 5.0
compressibility = 3e-4 3e-4
ref_p = 1.0 1.0
; GENERATE VELOCITIES FOR STARTUP RUN:
gen_vel = no
refcoord_scaling = all
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
; COM Pulling
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
pull = yes
pull-nstxout = 100
pull-nstfout = 100
pull-ngroups = 2
pull-group1-name = POPC
pull-group2-name = Protein
pull-ncoords = 1
pull-cylinder-r = 1.2
pull-coord1-k = <FC>
pull-coord1-type = umbrella
pull-coord1-geometry = cylinder
pull-coord1-groups = 1 2
pull-coord1-dim = N N Y
pull-coord1-vec = 0.0 0.0 1.0
pull-coord1-start = no
pull-coord1-rate = 0.00
pull_coord1_init = <CV>
Thank you so much in advance