Thank you Justin. It is weird I cannot reproduce it with the same mdp: 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 LIG_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
Using: grompp -f pull3nmSnew.mdp -c npt298.gro -p topol.top -n index.ndx -t npt298.cpt -o pullS_2new.tpr As I take velocities from npt it should be reproducible but profiles force vs time looks similar with breaking point at different time. Can I edit somehow tpr file and change the frequency of frames only? Otherwise I have to run pulling again and US windows from scratch... quite time consuming. Steven On Tue, Dec 25, 2012 at 1:28 PM, Justin Lemkul <[email protected]> wrote: > > > On 12/25/12 3:51 AM, Steven Neumann wrote: >> >> 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? >> > > Because, as I said, that's not what the -rerun function does. The -rerun > function simple re-evaluates the energies of the existing frames according > to the topology in the .tpr file, thus allowing you to re-calculate energy > terms based on new energy groups or a modified topology. If a frame does > not exist, you cannot create it magically. If you didn't save the frame you > needed, you need to run a new simulation. There is no way to interpolate > new frames. > > -Justin > > > -- > ======================================== > > 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 [email protected] > 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 [email protected]. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list [email protected] 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 [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
