I have tried 15,000 steps; I noticed that Fmax starts out at ~3.0e+03 and increases to ~1.2e+06 before coming down very slowly to ~5.0e+04. Additionally, letting the minimisation run for a long time gives me a "converged to machine precision, but not to Fmax < 10" message.
I am wondering why the Lysozyme tutorial at: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/index.html does not have the same problems? Is there a way to stop minimisation and continue later from that same point? Thanks, Nancy On Thu, Aug 6, 2009 at 6:45 PM, Justin A. Lemkul <[email protected]> wrote: > > > Nancy wrote: > > <snip> > > Note: the ethanediol.log file contains a section that has several lines >> with asterisks: >> >> ============================ >> Angles Force Field Results >> Angle Atoms force angle method measured >> 1 H12- C1- H11 ****** ****** ****** 109.403 >> > > Probably because these angles don't exist in a UA force field, as they > involve non-polar hydrogens. > > >> $ editconf -f ethanediol.gro -o ethanediol_box.gro -c -d 1.0 -bt cubic >> >> $ genbox -cp ethanediol_box.gro -cs spc216.gro -o ethanediol_solv.gro -p >> ethanediol.top >> >> $ grompp -f minim.mdp -c ethanediol_solv.gro -p ethanediol.top -o em.tpr >> >> the "minim.mdp" file is: >> >> ============================ >> define = -DFLEXIBLE >> integrator = steep >> emtol = 10.0 >> emstep = 0.01 >> nsteps = 2000 >> >> > Increase the value of nsteps dramatically. If you are aiming for Fmax < > 10, 2000 steps likely is not sufficient. Use a ridiculously high value, and > if mdrun completes all those steps without converging, keep increasing the > value. I typically set nsteps = 500000 to make sure the EM doesn't stop > before reaching emtol. If it does, then something may be wrong. > > nstlist = 1 >> ns_type = grid >> rlist = 1.0 >> coulombtype = PME >> rcoulomb_switch = 1.0 >> > > With PME, rcoulomb_switch is meaningless. > > rvdw_switch = 1.3 >> > > With the default vdwtype (cutoff), rvdw_switch is also meaningless. > > <snip> > > Steepest Descents did not converge to Fmax < 10 in 2001 steps. >> Potential Energy = -3.3810168e+04 >> Maximum force = 5.4957539e+04 on atom 559 >> Norm of force = 2.7119446e+03 >> ============================ >> >> I have already tried increasing the number of steps, but I found no way >> > > How many steps did you try? > > of lowering the forces. I have found that by limiting the number of >> solvent molecules to ~5, I can manage to acheive lower energies, however, >> the amount of time it takes for a larger number of water molecules increases >> exponentially. >> >> So, I am trying to proceed to equilibration: >> >> > Stop right here. It is a waste of time. If you EM does not converge, you > *cannot* force the system to run. It will explode, sooner or later. > Depending on how soon it does will determine how much time you waste. > > At this point, you are really getting the same advice over and over, > because the question is always the same, but the values of Fmax are > different. Can you post the topology you're using for this system, in > particular, the parameters for ethanediol? > > -Justin > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > 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/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/mailing_lists/users.php >
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