Thanks Mr.Mark for your reply, I am not getting any error, but after Position restrain step, when I see the structure of *pr_protein_popc_out.gro in VMD the POPC tails are tilting towards backwards(like pulling). It looks there is gap inbetween two membrane layers, middle part of the protein appears without covering POPC moledules, but water and protein structure are fine. Can you pls tell where is the problem ? Is there in any mistake in my * pr.mdp file I am gving description about what steps i have done: 1.The protein simulated in solution for 500ps . 2. Protein inserted into POPC by using "genbox". 3. Steepest gradient energy minimisation for "protein embedded in POPC system" , here strucure is fine 4. Postion restrain for same system - For Protein, POPC and Water force constant -10000 I have used.
I am mentioning my *pr.mdp file title = popc restrained define = -DPOSRES -DPOSRES_LIPID -DPOSRES_WATER 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 rlist = 0.9 coulombtype = PME rcoulomb = 0.9 rvdw = 1.4 pbc = xyz ; Berendsen temperature coupling is on in two groups Tcoupl = Berendsen tc-grps = POPC Protein SOL_Cl tau_t = 0.1 0.1 0.1 ref_t = 310 310 310 ; Anisotropic pressure coupling is now on Pcoupl = berendsen pcoupltype = anisotropic tau_p = 1.0 1.0 1.0 1.0 1.0 1.0 compressibility = 4.5e-5 4.5e-5 4.5e-5 0 0 0 ref_p = 1.0 1.0 1.0 1.0 1.0 1.0 ; Energy monitoring energygrps = POPC Protein SOL_Cl ; Generate velocites is on at 300 K. gen_vel = yes gen_temp = 310 gen_seed = 173529 Thanks in advance.
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