[gmx-users] How to increase the tolerance for conjugate gradient minimization

[Ran Friedman]

Hi Arthur,

The most useful option from my experience is to run Gromacs in double
precision.
You also can try to make emstep smaller (after an initial minimisation
of the crude structure) and use l-bfgs.

Good luck,
Ran

-- 
------------------------------------------------------
Ran Friedman
Postdoctoral Fellow
Computational Structural Biology Group (A. Caflisch)
Department of Biochemistry
University of Zurich
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CH-8057 Zurich, Switzerland
Tel. +41-44-6355559
Email: r.friedman at bioc.uzh.ch
Skype: ran.friedman
------------------------------------------------------

Arthur Roberts wrote:
> I agree the code is fine.  Is there a parameter that I need to change
> to increase the tolerance?  I have issues energy minimizing a small
> molecule in the presence of a macromolecule.  One work around is to
> increase the energy of the small molecule, so that the macromolecule
> no longer dominates the energetics.  I would appreciate your input.
>
> Art
>
> On Jun 4, 2010, at 5:45 PM, Mark Abraham wrote:
>
>>
>>
>> ----- Original Message -----
>> From: Arthur Roberts <aroberts99163 at yahoo.com>
>> Date: Saturday, June 5, 2010 4:57
>> Subject: [gmx-users] How to increase the tolerance for conjugate
>> gradient minimization
>> To: gmx users <gmx-users at gromacs.org>
>>
>> > Hi, all,
>> >
>> > Is there a way to increase the tolerance for Conjugate Gradient
>> > energy minimization?
>> >
>> > It seems that I can only get a Tolerance (Fmax) = 1e-4
>> >
>> > emtol doesn't seem to do the trick.  I tried several values.
>>
>> The code's fine in 4.0.7. Does your .mdp value match that reported in
>> the .log file? Ditto in gmxcheck on the .tpr?
>>
>> Mark --
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>
> Art Roberts
> 7254 Shoreline Dr. #130
> San Diego, CA 92122
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> email: aroberts99163 at yahoo.com
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