[gmx-users] Very High Forces During Minimisation

[Nancy]

 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 <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 | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
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