Dear Dr. Warren Unfortunately,I missed your reply! 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 [image: Mailtrack] <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality5&;> Sender notified by Mailtrack <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality5&;> 09/25/19, 03:36:23 PM On Tue, Sep 24, 2019 at 1:20 PM Mahsa Rezaei <mahsarezaei94...@gmail.com> 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 > > > [image: Mailtrack] > <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality5&;> > Sender > notified by > Mailtrack > <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality5&;> > 09/24/19, > 01:19:54 PM > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
