Hi all, I embedded protein into membrane. After that *EM and *PR running fine but in position restrian intial step, one side of the membrane layer, water molecules move to second side although total structure looks cubic form, Only problem with diplacemnt of water to otehrside. Shall I run it for longer time? I may get equal number of water molecules both sides.
I am pasting my pr.mdp file (Fc on protein 1000) title = dpt pos restrained define = -DPOSRES constraints = all-bonds integrator = md dt = 0.002 ; ps ! nsteps = 10000 ; total 50 ps. nstcomm = 1 nstxout = 50 nstvout = 1000 nstfout = 0 nstlog = 10 nstenergy = 10 nstlist = 10 ns_type = grid coulombtype = PME rlist = 0.9 rcoulomb = 0.9 rvdw = 1.4 pbc = xyz ; Berendsen temperature coupling is on in two groups Tcoupl = berendsen tc-grps = Protein POPC SOL_Cl tau_t = 0.1 0.1 0.1 ref_t = 310 310 310 ; isotropic pressure coupling is now on Pcoupl = parrinello-rahman pcoupltype = anisotropic tau_p = 1.0 1.0 1.0 0 0 0 compressibility = 4.5e-5 4.5e-5 4.5e-5 0 0 0 ref_p = 1.0 1.0 1.0 0 0 0 ; Energy monitoring energygrps = Protein POPC Sol_Cl ; Generate velocites is on at 300 K. gen_vel = yes gen_temp = 310 gen_seed = 173529 Pls help me Thanks in advance
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