On Tue, Dec 25, 2012 at 2:58 AM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 12/24/12 5:53 PM, Steven Neumann wrote: >> >> Dear Gmx Users, >> >> I run pulling simulation of my ligand away from the protein. I >> produced 1500 frames and run US windows with 0.1 nm spacing. However, >> I have a gap in histograms - I need to use lower value of nstxtcout to >> get the proper window where the gap is as the time it goes away is >> really short. >> >> How can I rerun the same trajectory with lower nstxtcout ? I do not >> want to use grompp as from the same mdp file with pulling simulation I >> get different trajectories. My mdp (it is continuation after nvt and >> npt respectively): >> >> title = Umbrella pulling simulation >> define = -DPOSRES_T >> ; Run parameters >> integrator = md >> dt = 0.002 >> tinit = 0 >> nsteps = 150000 ; 0.3 ns >> nstcomm = 10 >> ; Output parameters >> nstxout = 0 >> nstvout = 0 >> nstxtcout = 100 ; every 1 ps 1500 frames >> nstenergy = 500 >> ; Bond parameters >> constraint_algorithm = lincs >> constraints = all-bonds >> continuation = yes ; continuing from NPT >> ; Single-range cutoff scheme >> nstlist = 5 >> ns_type = grid >> rlist = 1.4 >> rcoulomb = 1.4 >> rvdw = 1.2 >> vdwtype = Switch >> rvdw-switch = 1.0 >> ; PME electrostatics parameters >> coulombtype = PME >> fourierspacing = 0.12 >> fourier_nx = 0 >> fourier_ny = 0 >> fourier_nz = 0 >> pme_order = 4 >> ewald_rtol = 1e-5 >> optimize_fft = yes >> ; Temperature coupling is on >> tcoupl = V-rescale ; modified Berendsen >> thermostat >> tc_grps = Protein FE_Water_and_ions ; two coupling groups - more >> accurate >> tau_t = 0.1 0.1 ; time constant, in ps >> ref_t = 298 298 ; reference temperature, >> one for each group, in K >> ; Pressure coupling is on >> Pcoupl = Parrinello-Rahman >> pcoupltype = isotropic >> tau_p = 2.0 >> compressibility = 4.5e-5 >> ref_p = 1.0 >> ; Generate velocities is off >> gen_vel = no >> ; Periodic boundary conditions are on in all directions >> pbc = xyz >> ; Long-range dispersion correction >> DispCorr = EnerPres >> ; Pull code >> pull = umbrella >> pull_geometry = distance ; simple distance increase >> pull_dim = N N Y >> pull_start = yes ; define initial COM distance > 0 >> pull_ngroups = 1 >> pull_group0 = GLU >> pull_group1 = LIG >> pull_rate1 = 0.01 ; 0.001 nm per ps = 1 nm per ns >> pull_k1 = 2000 ; kJ mol^-1 nm^-2 >> >> Shall I use rerun option of mdrun? But I wont be able to change >> frequency of frames. >> > > You can't create frames that aren't there, unfortunately. Saving every 0.2 > ps is usually vast overkill; if you have a gap in the sampling, you probably > need more windows rather than more frames in the existing ones. > > -Justin
O course I know! This is why I want to rerun my pulling simulation to get more frames for umbrella sampling windows and no to waste windows I have already run - hence I need exactly the same trajectory. grompp -f new.mdp ... -o new.tpr mdrun -s new.tpr -rerun oldPull.xtc -deffnm new Is that correct? > > -- > ======================================== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > 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
