Hello sir, Thanks for such a explanatory tutorial. I am stuck with one error now. I have protein, popc, sol and cl- in my system. I have merged the sol and cl- using make_ndx. But when I run grompp I get the error like this "popc not defined in the index file". The grompp command : grompp -f pr.mdp -c box_em.pdb -p topol.top -o box_pr.tpr Any suggestions please. * pr.mdp file :* title = protein in popc bilayer cpp = /usr/bin/cpp define = -DPOSRES -DPOSRES_LIPID constraints = all-bonds constraint-algorithm= Lincs integrator = md dt = 0.002 nsteps = 5000 nstcomm = 1 nstxout = 50 nstvout = 1000 nstfout = 0 nstlog = 10 nstenergy = 10 nstlist = 10 ns_type = grid rlist = 1 coulombtype = PME rcoulomb = 1 vdw-type = Cut-off rvdw = 1 ; Berendsen temperature coupling is on in two groups tcoupl = berendsen tc_grps = Protein POPC SOL_CL- tau_t = 0.1 0.1 0.1 ref_t = 300 300 300 ; Energy monitoring energygrps = Protein POPC SOL_CL- ; Pressure coupling is on ;Pcoupl = berendsen tau_p = 2.0 2.0 compressibility = 4.5e-5 4.5e-5 ref_p = 1.0 1.0 Pcoupl_type = semiisotropic ; Generate velocites is on at 300 K. gen_vel = yes gen_temp = 300.0 gen_seed = 173529
Thanking you, Pawan
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