Dear gmx-users, <br>I have inserted my protein into membrane. I did energy minimisation with Steepest descent, that output used for input of position restrain, this "EM out.gro" structure is fine . When I do Position restrain, this step goes fine but, popc structure of " PR out.gro " looks tilted. Where is the error happening?<br>
I am mentioning my pr.mdp file <br>Pls help me. Thanks in advance<br><br>title = Protein in popc 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>nstlog = 10<br>nstenergy = 10<br>
nstlist = 10<br>ns_type = grid<br>rlist = 0.9<br>coulombtype = PME<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 = POPC Protein SOL_Cl<br>tau_t = 0.1 0.1 0.1<br>ref_t = 310 310 310<br>; Anisotropic pressure coupling is now on<br>
Pcoupl = berendsen<br>pcoupltype = anisotropic<br>tau_p = 1.0 1.0 1.0 1.0 1.0 1.0<br>compressibility = 4.5e-5 4.5e-5 4.5e-5 0 0 0<br>ref_p = 1.0 1.0 1.0 1.0 1.0 1.0<br>
; Energy monitoring<br>energygrps = POPC Protein SOL_Cl<br>; Generate velocites is off at 300 K.<br>gen_vel = yes<br>gen_temp = 310<br>gen_seed = 173529<br>~ <br>
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