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 <[email protected]
<mailto:[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 <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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