Dear All, I have done a simulation (in water) of PfPBGD model protein for 500 ps. But when I compared the secondary structure of my native protein structure vs structure after simulation. I observed that lot of unfolding is happening after simulation. So, my queries are: 1> Is there any way I can improve my model so that model protein become stable? 2> Is there any problem with my parameters which i have used for energy minimization, Position restrained dynamics and final simulation? 3> Can I improve my result changing the parameter files?
what are the changes required? These are the parameters I have used for different run: em.mdp: cpp = /usr/bin/cpp define = -DFLEX_SPC constraints = none integrator = steep dt = 0.002 ;ps nsteps = 400 ; ; Energy minimizing stuff ; emtol = 2000 emstep = 0.01 nstcomm = 1 ns_type = grid rlist = 1 rcoulomb = 1.0 rvdw = 1.0 Tcoupl = no Pcoupl = no gen_vel = no pr.mdp: title = Yo cpp = /usr/bin/cpp define = -DPOSRES constraints = all-bonds integrator = md dt = 0.002 ; ps ! nsteps = 10000 ; total 20 ps. nstcomm = 1 nstxout = 50 nstvout = 1000 nstfout = 0 nstlog = 10 nstenergy = 10 nstlist = 10 ns_type = grid rlist = 1.0 coulombtype = PME rcoulomb = 1.0 rvdw = 1.4 ; Berendsen temperature coupling is on in two groups Tcoupl = berendsen tc-grps = Protein SOL CL- tau_t = 0.1 0.1 0.1 ref_t = 300 300 300 ; Energy monitoring energygrps = Protein SOL CL- ; Pressure coupling is not on Pcoupl = no tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp = 300.0 gen_seed = 173529 full.mdp: title = Yo cpp = /usr/bin/cpp constraints = all-bonds integrator = md dt = 0.002 ; ps ! nsteps = 250000 ; total 500 ps. nstcomm = 1 nstxout = 250 nstvout = 1000 nstfout = 0 nstlog = 100 nstenergy = 100 nstlist = 10 ns_type = grid rlist = 1.0 rcoulomb = 1.0 rvdw = 1.0 ; Berendsen temperature coupling is on in two groups Tcoupl = berendsen tc-grps = Protein SOL CL- tau_t = 0.1 0.1 0.1 ref_t = 300 300 300 ; Energy monitoring energygrps = Protein SOL CL- ; Isotropic pressure coupling is now on Pcoupl = berendsen Pcoupltype = isotropic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is off at 300 K. gen_vel = no gen_temp = 300.0 gen_seed = 173529 I expect suggestion from expert. Thanks, Sukesh _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
