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
========================================
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