[gmx-users] Re: Minimization not converging

[Justin A. Lemkul]

Jack Shultz wrote:
> I should have included some output
> 
> Step=   32, Dmax= 2.4e-06 nm, Epot= -1.03223e+05 Fmax= 3.87326e+06, atom= 25439
> Step=   33, Dmax= 1.2e-06 nm, Epot= -1.03222e+05 Fmax= 3.87334e+06, atom= 25439
> Stepsize too small, or no change in energy.
> Converged to machine precision,
> but not to the requested precision Fmax < 10
> 
> Double precision normally gives you higher accuracy.
> You might need to increase your constraint accuracy, or turn
> off constraints alltogether (set constraints = none in mdp file)
> 
> writing lowest energy coordinates.
> 
> Steepest Descents converged to machine precision in 34 steps,
> but did not reach the requested Fmax < 10.
> Potential Energy  = -1.4354568e+06
> Maximum force     =  6.9535597e+10 on atom 25439
> Norm of force     =  4.5592896e+08
> 
> More details here.
> http://www.hydrogenathome.org/result.php?resultid=1291344
> 

 From your pdb2gmx output, it looks like you have some lousy starting geometry 
in whatever structure you're processing:

http://wiki.gromacs.org/index.php/Errors#Long_bonds_and.2For_missing_atoms

Try to run EM on that structure before solvating (i.e., in vacuo) , because you 
probably have lots of steric clashes with the solvent arising because of 
improper protein geometry.

-Justin

> On Thu, Mar 12, 2009 at 10:59 AM, Jack Shultz
> <jshultz at hydrogenathome.org> wrote:
>> Hi,
>>
>> I think that my minimization are not running long enough. I've been
>> following the parameters in tutorials but it seems like they all die
>> at 34 steps
>>
>> I've been using these tutorials
>> https://extras.csc.fi/chem/courses/gmx2007/tutorial1/tutorial1.pdf
>> http://md.chem.rug.nl/education/mdcourse/MDpract.html
>>
>> Its been the same case for me regardless to whether I use Windows or
>> Linux platforms. Are there settings I can use to make the simulation
>> minimize longer or is this case where I need to have double precision
>> version?
>>
>> --
>> Jack
>>
>> http://www.facebook.com/home.php#/profile.php?id=832713248
>> http://hydrogenathome.org
>>
> 
> 
> 

-- 
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Justin A. Lemkul
Graduate Research Assistant
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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