On Wed, Jun 27, 2012 at 1:51 PM, Justin A. Lemkul <[email protected]> wrote: > > > On 6/27/12 7:48 AM, Steven Neumann wrote: >> >> Dear Gmx Users, >> >> I obtained a protein-ligand complex from 100ns simulation. Now I am >> pulling my ligand away from the protein after the energy minimzation >> in water and equilibration of 100ps (two coupling baths: Protein, >> LIG_Water_and_ions). >> Then I proceed my pulling : >> >> grompp -f pull.mdp -c npt.gro -p topol.top -n index.ndx -t npt.cpt -o >> pull.tpr >> >> mdrun -s pull.tpr -deffnm pull >> >> >> title = Umbrella pulling simulation >> define = -DPOSRES >> ; Run parameters >> integrator = md >> dt = 0.002 >> tinit = 0 >> nsteps = 500000 ; 1 ns >> nstcomm = 10 >> ; Output parameters >> nstxout = 0 >> nstvout = 0 >> nstfout = 500 >> nstxtcout = 1000 ; every 1 ps >> 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 = Protein >> pull_group1 = LIG >> pull_rate1 = 0.004 ; 0.004 nm per ps = 4 nm per ns >> pull_k1 = 500 ; kJ mol^-1 nm^-2 >> >> I run 3 pulling simulations with the same mdp and I obtain 3 >> different profiles (Force vs time). Then I used 2xlonger pulling with >> the same pulling distance and I run 3 simulations again. Each time I >> obtain different profile. Can anyone explain me this? I am using >> velocities from npt simulation as above (gen_vel = no and continuation >> = yes) so I presume the output should be similar. Please, advice. >> > > I assume you're passing a checkpoint file to grompp? If you're relying on > velocities from the .gro file, they are of insufficient precision to > guarantee proper continuation.
Thank you Justin. I am using according to your tutorial: grompp -f pull.mdp -c npt.gro -p topol.top -n index.ndx -t npt.cpt -o pull.tpr mdrun -s pull.tpr -deffnm pull Would you suggest: grompp -f pull.mdp -c npt.gro -p topol.top -n index.ndx -t npt.cpt -o pull.tpr mdrun -s pull.tpr -cpi npt.cpt -deffnm pull ?? Profiles do not vary slightly - the maximum pulling force (breaking point) varies from 290 to 500 kJ/mol nm2 which is really a lot. Steven > > Small variations are inherent in any simulation set, and in the case of > pulling, small changes (though intentional) are the basis for Jarzynski's > method. In any case, all MD simulations are chaotic and so it depends on > what your definition of "different" is in the context of whether or not > there are meaningful changes imparted through the course of each simulation. > Also note that in the absence of the -reprod flag, the same .tpr file may > result in a slightly different outcome. The implications of these outcomes > are limited by sampling; the ensemble should converge with sufficient time > and/or replicates. For non-equilibrium processes like pulling, convergence > is probably harder, but again you have to ask whether the differences are > meaningful. > > http://www.gromacs.org/Documentation/Terminology/Reproducibility > > -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 > * Only plain text messages are allowed! > * 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 * Only plain text messages are allowed! * 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
