[gmx-users] Very High Forces During Minimisation

[Justin A. Lemkul]

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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