Hi,
I have been trying to study folding of a peptide 24 residues long. I did a simulation of 50 ns with explicit solvent, CHARMM FF, but I was not able to find even a single folding event. Then I decided use explicit solvent for simulation and I again simulated the peptide for 100 ns . This time again I ended with no folding events. I know that in case of explicit solvent , a 50ns simulation time is not enough to observe anything. But I did it to see the initial behavior of the peptide in water. In take many random like conformation but doesnot fold into a desired beta-hairpin. For the explicit solvent simulation, I followed the lysozyme tutorial parameters. For implicit solvent simulation, I used the following parameters for Energy minimization : define = -DFLEXIBLE constraints = none integrator = steep dt = 0.001 ; ps nsteps = 30000 vdwtype = cut-off coulombtype = cut-off pbc = no nstlist = 0 ns_type = simple rlist = 0 ; this means all-vs-all (no cut-off), which gets expensive for bigger systems rcoulomb = 0 rvdw = 0 comm-mode = angular comm-grps = Protein optimize_fft = yes ; ; Energy minimizing stuff ; emtol = 5.0 emstep = 0.01 ; ; Implicit solvent ; implicit_solvent = GBSA gb_algorithm = Still ; HCT ; OBC nstgbradii = 1 rgbradii = 0 ; [nm] Cut-off for the calculation of the Born radii. Currently must be equal to rlist gb_epsilon_solvent = 80 ; Dielectric constant for the implicit solvent ; gb_saltconc = 0 ; Salt concentration for implicit solvent models, currently not used sa_algorithm = Ace-approximation sa_surface_tension = -1 For MD I used the following : - define = -DPOSRESHELIX ; -DFLEXIBLE -DPOSRES constraints = none integrator = md dt = 0.001 ; ps nsteps = 1000000000 ; 100000 ps = 100 ns nstcomm = 10 nstcalcenergy = 10 nstxout = 1000 ; frequency to write coordinates to output trajectory nstvout = 0 ; frequency to write velocities to output trajectory; the last velocities are always written nstfout = 0 ; frequency to write forces to output trajectory nstlog = 1000 ; frequency to write energies to log file nstenergy = 1000 ; frequency to write energies to edr file vdwtype = cut-off coulombtype = cut-off pbc = no nstlist = 0 ns_type = simple rlist = 0 ; this means all-vs-all (no cut-off), which gets expensive for bigger systems rcoulomb = 0 rvdw = 0 comm-mode = angular comm-grps = system optimize_fft = yes ; V-rescale temperature coupling is on Tcoupl = v-rescale tau_t = 0.1 tc_grps = system ref_t = 300 ; Pressure coupling is off Pcoupl = no ; Generate velocites is on gen_vel = yes gen_temp = 300 gen_seed = -1 ; ; Implicit solvent ; implicit_solvent = GBSA gb_algorithm = Still ; HCT ; OBC nstgbradii = 1 rgbradii = 0 ; [nm] Cut-off for the calculation of the Born radii. Currently must be equal to rlist gb_epsilon_solvent = 80 ; Dielectric constant for the implicit solvent ; gb_saltconc = 0 ; Salt concentration for implicit solvent models, currently not used sa_algorithm = Ace-approximation sa_surface_tension = -1 So, finally I want to know where have I gone in my simulation experiments, both implicit and explicit ?? ... Please reply . ---------------- BHARAT -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
