[gmx-users] Umbrella sampling on lipid bilayer

[Mahsa Rezaei]

Dear Dr. Warren

Thanks for your response .

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 .

Thank you .

Regards

Mahsa.



Does it do that without using the pull code, i.e. just performing NPT
simulation? What is physically happening? Sounds like the bilayer is
unstable. What forcefield is this?

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052dallas.warren at monash.edu
<https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users>
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a
nail.


On Tue, 24 Sep 2019 at 19:50, Mahsa Rezaei <mahsarezaei94.mr at
gmail.com <https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users>>
wrote:

>* 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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