[gmx-users] Umbrella sampling on lipid bilayer
mahsarezaei94.mr at gmail.com
Sun Sep 29 17:04:14 CEST 2019
Dear gromacs users,
Sorry for repeating my question.
I didn't receive any email so I couldn't reply and I missed
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.
I made my protein-membrane system with charmm-gui.
so my force is charmm36.
I used the equilibration input files that charmm-gui provide ,
and run 400 ns simulation for equilibration of my system .
RMSD , temperature and pressure is good , so I think my system is stable .
Every thing is good until I use following pull code in my mdp file .
The bilayer does not move and the ligand passes through the membrane
But over time , the length of the z axis increases , and
4 water molecules are also separated from the membrane.
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
pull_group1_name = BILAYER
pull_group2_name = LIG
pull_coord1_type = umbrella ; harmonic potential
pull_coord1_geometry = direction
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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