[gmx-users] Umbrella sampling on lipid bilayer

Justin Lemkul jalemkul at vt.edu
Wed Sep 25 14:58:18 CEST 2019 


On 9/25/19 5:50 AM, Mahsa Rezaei wrote:
> 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 .

Distortion of membrane protein systems (elongation or compaction along 
the z-axis) with CHARMM is a bug that was recently fixed. You can either 
patch the code with the fix found at 
https://gerrit.gromacs.org/c/gromacs/+/13297 or wait for the next 
release in any of the 2018, 2019, or 2020 branches and re-run your 
simulations.

-Justin

> 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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-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

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