Maybe I wrote it wrote it wrong. I have 1500 frames of which with 0.1 nm spacing I have chosen 14 to run umbrella sampling windows.
I used: conf0.gro conf140.gro conf213.gro conf262.gro conf263.gro conf300.gro ... conf1500.gro However, the moment when my ligand became dettached is very short (beween conf conf262.gro and 263.gro) that there is a gap in histograms. So I need the same pulling trajectory but with more frames e.g. 10 times higher. when I use grommp -f new.mdp -o new.tpr mdrun -rerun oldPull.xtc -s new.tpr -deffnm new I dont get my new.xtc ... Hoiw can I solve it? Steven On Tue, Dec 25, 2012 at 8:27 AM, Steven Neumann <s.neuman...@gmail.com> wrote: > 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
