Hi all,<br>my protein contain 59 aminoacid residues and crstal water molecules 103,<br> The steps i have done are <br>1.minimisation of protein invacuo<br>2.added simulation box of 6 in xyz dimensions<br>3.added water <br>
4.added ions<br>5.energy minimisation in water<br>6.positoin restrain in water<br>7.production step......<br>My sytem is fine till 250 ps production , after that protein is coming to outside from water box, <br> whats the problem ?<br>
have i done any mistake while doing steps or any mistake in md.mdp file<br>pls help me...<br>along with my mail, md.mdp file is attaching here,<br><u>md.mdp</u><br>title = dpt_prod<br>constraints = hbonds<br>
integrator = md<br>dt = 0.002 ; ps !<br>nsteps = 125000 ; total 250 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>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 Sol CL-<br>tau_t = 0.1 0.1 0.1<br>ref_t = 300 300 300<br>
; isotropic pressure coupling is now on<br>Pcoupl = Berendsen<br>pcoupltype = isotropic<br>tau_p = 1.0<br>compressibility = 4.5e-5<br>ref_p = 1.0<br>; Energy monitoring<br>
energygrps = Protein Sol CL-<br>; Generate velocites is on at 300 K.<br>gen_vel = yes<br>gen_temp = 300<br>gen_seed = 173529<br> 39,1 Bot<br>
Thanks in advance.<br><br>