Dear gromacs users, Sorry for repeating my question.
I didn't receive any email so I couldn't reply and I missed them. 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 [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&> 09/29/19, 06:33:51 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.