Hi all, <br>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.<br>
<br>I am pasting my pr.mdp file (Fc on protein 1000)<br><br>title = dpt pos restrained<br>define = -DPOSRES<br>constraints = all-bonds<br>integrator = md<br>dt = 0.002 ; ps !<br>
nsteps = 10000 ; total 50 ps.<br>nstcomm = 1<br>nstxout = 50<br>nstvout = 1000<br>nstfout = 0<br>nstlog = 10<br>nstenergy = 10<br>
nstlist = 10<br>ns_type = grid<br>coulombtype = PME<br>rlist = 0.9<br>rcoulomb = 0.9<br>rvdw = 1.4<br>pbc = xyz<br>; Berendsen temperature coupling is on in two groups<br>
Tcoupl = berendsen<br>tc-grps = Protein POPC SOL_Cl<br>tau_t = 0.1 0.1 0.1<br>ref_t = 310 310 310<br>; isotropic pressure coupling is now on<br>
Pcoupl = parrinello-rahman<br>pcoupltype = anisotropic<br>tau_p = 1.0 1.0 1.0 0 0 0<br>compressibility = 4.5e-5 4.5e-5 4.5e-5 0 0 0<br>ref_p = 1.0 1.0 1.0 0 0 0<br>
; Energy monitoring<br>energygrps = Protein POPC Sol_Cl<br>; Generate velocites is on at 300 K.<br>gen_vel = yes<br>gen_temp = 310<br>gen_seed = 173529<br><br>Pls help me <br>
Thanks in advance<br>