Thanks for the reply Justin,
> > In theory, that should work. Please post the entirety of your .mdp file. > > Have you done any prior equilibration, or have you moved straight into > annealing? I would suggest a restrained NVT before applying NPT or > annealing > when using the restraints. > Yes I did the restrained NVT before but the same problem came, morover there was a hole in the upper part of the system with the SOL molecules displaced. So then I tried to run the annealing but in this case the SOL molecules were intact but similar problem came with the lipid membrane. though, just to check then I tried to equilibration with restrained NVT where I restrained the movement of the lipid in all the x, y, z axis the problem did not occur. Here is my mdp file -------------------------------------------------------------------------- title = NVT equilibration for B3-DPPC define = -DPOSRES -DPOSRES_LIPID ; position restrain the protein and lipid ; 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- -------------------------------------------------------------------------- This is the topology file: -------------------------------------------------------------------------- ;Include DPPC chain topology #include "dppc.itp" #ifdef POSRES_LIPID ; Position restraint for each lipid #include "lipid_posre.itp" #endif ; Include water topology #include "spc.itp" #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcx fcy fcz 1 1 1000 1000 1000 #endif ; Include generic topology for ions #include "ions.itp" [ system ] ; Name protein 128-Lipid DPPC Bilayer [ molecules ] ; Compound #mols Protein_A 1 DPPC 121 SOL 9867 CL- 14 -------------------------------------------------------------------------- thanks Parul Tewatia
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