[gmx-users] Umbrella sampling on lipid bilayer

[John Whittaker]

> Dear gromacs users,
>
> Sorry for repeating my question.
>
> I didn't receive any email so I couldn't reply and I missed
>
> them.

Hi,

Justin replied in this mail:
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2019-September/126735.html

Best,

John

>
> 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
> coordinate
> 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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