gmx-users@gromacs.org Dear Gmx users,
I am working on a transmembrane protein and my system contains protein, DPPC bilayer, water (spc) and ions. After preparing my system for simulation I have successfully performed the energy minimization, I am facing a problem at the nvt equilibration phase of 100ps, the lipid molecules enter the voids in the solvent leaving the protein naked. I have already used position restraint at the inflate.gro steps, now I have read that I can use the option to freeze the groups which I can do at the z axis to avoid the lipid headgroups to enter the void of the solvent. The manual suggests starting with freezing in a constant volume simulation and afterwards using position restraints in conjunction with constant pressure. Now, Is it feasible if I freeze the lipids in z-axis for the whole course of simulation or should I do it only during the equilibration phase? Is there any alternative which I can use during simulation to avoid this? My nvt.mdp is: ----------------------------------------------------------- title = NVT equilibration for B3-DPPC define = -DPOSRES ; position restrain the protein ; Run parameters integrator = md ; leap-frog integrator nsteps = 50000 ; 2 * 50000 = 100 ps dt = 0.002 ; 2 fs ; Output control nstxout = 100 ; save coordinates every 0.2 ps nstvout = 100 ; save velocities every 0.2 ps nstenergy = 100 ; save energies every 0.2 ps nstlog = 100 ; update log file every 0.2 ps ; Bond parameters continuation = no ; first dynamics run constraint_algorithm = lincs ; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching ns_type = grid ; search neighboring grid cels nstlist = 5 ; 10 fs rlist = 1.2 ; short-range neighborlist cutoff (in nm) rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm) rvdw = 1.2 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling is on tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = Protein DPPC SOL_CL- ; three coupling groups - more accurate tau_t = 0.1 0.1 0.1 ; time constant, in ps ref_t = 323 323 323 ; reference temperature, one for each group, in K ; Pressure coupling is off pcoupl = no ; no pressure coupling in NVT ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr = EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = yes ; assign velocities from Maxwell distribution gen_temp = 323 ; temperature for Maxwell distribution gen_seed = -1 ; generate a random seed ; COM motion removal ; These options remove motion of the protein/bilayer relative to the solvent/ions nstcomm = 1 comm-mode = Linear comm-grps = Protein_DPPC SOL_CL- ---------------------------------------------------------------------------------------- thanks, Parul Tewatia
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