On Wed, May 22, 2013 at 2:19 AM, bharat gupta <bharat.85.m...@gmail.com>wrote:
> 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 > > These are the same data. Whatever you are doing to generate them isn't what you think you're doing :-) Mark > 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 > -- 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