[gmx-users] Umbrella sampling on lipid bilayer

[Mahsa Rezaei]

Dear gromacs users,

I am using following pull code in md simulation
for pulling a ligand across the plasma membrane model.
Ligand passes through the membrane,but along simulation,
the size of axis z increases.
My size box is 8.52807   8.52807  14.00000.
And the pull distance is less than one-half the length of the box vector
along.pull distance is 6 nm.
After simulation my size box is 8.09025   8.09025  91.84508.
What should I do?

I would be very appreciated for your such kind helps.

My mdp file  :
title                   = Umbrella pulling simulation
; Run parameters
integrator              = md
dt                      = 0.002
tinit                   = 0
nsteps                  = 300000 ; 600 ps

; Output parameters
nstlog                  = 1000
nstxout                 = 500   ; every 1 ps
nstvout                 = 500
nstfout                 = 500
nstxtcout               = 500    ; every 1 ps
nstcalcenergy           = 500
nstenergy               = 500
; PME electrostatics parameters
coulombtype             = pme
; Single-range cutoff scheme
cutoff-scheme           = Verlet
nstlist                 = 20
rlist                   = 1.2
rcoulomb                = 1.2
vdwtype                 = Cut-off
vdw-modifier            = Force-switch
rvdw_switch             = 1.0
rvdw                    = 1.2
; Berendsen tempearture coupling is on in two groups
tcoupl                  = nose-hoover
tc_grps                 = Protein_LIG TIP3_CLA DOPC
tau_t                   = 1.0    1.0   1.0
ref_t                   = 303.15 303.15 303.15
; Pressure coupling is on
pcoupl                  = Parrinello-Rahman
pcoupltype              = semiisotropic
tau_p                   = 5.0
compressibility         = 4.5e-5  4.5e-5
ref_p                   = 1.0     1.0
refcoord_scaling        = com
; Bond parameters
constraints             = h-bonds
constraint_algorithm    = LINCS
continuation            = yes
;
nstcomm                 = 100
comm_mode               = linear
comm_grps               = Protein_LIG TIP3_CLA DOPC
; Generate velocities is off
gen_vel                 = no
; Periodic boundary conditions are on in all directions
pbc                     = xyz

; Pull code
pull                    = yes
pull_ncoords            = 1         ; only one reaction coordinate
pull_ngroups            = 2         ; two groups defining one reaction
coordinate
pull_group1_name        = BILAYER
pull_group2_name        = LIG
pull_coord1_type        = umbrella  ; harmonic potential
pull_coord1_geometry    = direction
pull_coord1_dim         = N N Y
pull_coord1_vec         = 0 0 1
pull_coord1_groups      = 1 2
pull_coord1_start       = yes       ; define initial COM distance > 0
pull_coord1_rate        = 0.01      ; 0.01 nm per ps =10nm per ns
pull_coord1_k           = 2000      ; kJ mol^-1 nm^-2
pull_nstxout            = 500        ; every 1 ps
pull_nstfout            = 500        ; every 1 ps


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09/24/19,
01:19:54 PM