[gmx-users] Umbrella sampling on lipid bilayer
johnwhittake at zedat.fu-berlin.de
Mon Sep 30 11:09:52 CEST 2019
> Dear gromacs users,
> Sorry for repeating my question.
> I didn't receive any email so I couldn't reply and I missed
Justin replied in this mail:
> 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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