Dear Sir, I performed another round of trial with different set of temperature and I got the avg accp. ration around 0.22. Here's the temp. dist. that I used : 250 268 288 308 331 355 380 408 438 469 503 540 579 621
I then checked the replica_index and replica_temp files for each replica individually. The plots are exactly similar for all the replicas, as an eg. here's the link for first three replicas . https://www.dropbox.com/s/cuydj010wh2hgkt/replica_index0.png https://www.dropbox.com/s/q01wluh8wxlcxs8/replica_index1.png https://www.dropbox.com/s/cm9f8qo1afo6w4k/replica_index2.png https://www.dropbox.com/s/gkbu0g0e1r37l57/replica_temp0.png https://www.dropbox.com/s/sffq8rwghjublu0/replica_temp1.png https://www.dropbox.com/s/ulccw8xabj66ktm/replica_temp2.png I checked the PE overlap also, that looks fine ( https://www.dropbox.com/s/0qf06of9lp1m51d/pe_overlap.png) I checked for the temp. dist. which also looks fine to me . https://www.dropbox.com/s/ed66uop16blgqwa/temp_dist.png I don't know why all plots are similar ?? Is this related to wrong settings in mdp file. Here's the mdp file that I am using for production run. I changed ref_t for each replica in the mdp file. I suspect that I am doing something wrong somewhere ... define = -DPOSRESHELIX ; -DFLEXIBLE -DPOSRES constraints = all-bonds integrator = md dt = 0.002 ; ps nsteps = 25000000; 50000 ps = 50 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 = 250 ; 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 = 78.5 ; 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 = 0.005 It will be helpful if you provide your comments... Regards -------------- BHARAT -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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