[gmx-users] Very High Forces During Minimisation
Justin A. Lemkul
jalemkul at vt.edu
Fri Aug 7 01:15:30 CEST 2009
Nancy wrote:
> 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.
>
And is that Fmax always on the order of 5e+4? An Fmax of 10 is very low, most
systems run with single-precision will not reach this value.
> 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?
>
Because when I wrote the tutorial, I chose a system that would reliably
energy-minimize: a well-defined protein structure from a high-quality model,
surrounded by only water. Such systems routinely converge to Fmax < 1000, much
less rigorous than what it seems you are trying to do.
Note that just because one tutorial works with a protein in water, that does not
mean all systems will inherently be problem-free.
> Is there a way to stop minimisation and continue later from that same point?
>
You can try to extend it like any other simulation:
http://oldwiki.gromacs.org/index.php/Extending_Simulations
-Justin
> Thanks,
>
> Nancy
>
> On Thu, Aug 6, 2009 at 6:45 PM, Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> 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 <http://vt.edu> | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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--
========================================
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
========================================
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