Dear gmx-users, 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? I am mentioning my pr.mdp file Pls help me. Thanks in advance
title = Protein in popc restrained define = -DPOSRES constraints = all-bonds integrator = md dt = 0.002 ; ps ! nsteps = 10000 ; total 50 ps. nstcomm = 1 nstxout = 50 nstvout = 1000 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 off at 300 K. gen_vel = yes gen_temp = 310 gen_seed = 173529 ~ ~
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