[gmx-users] Energy Minimization Problems

[David van der Spoel]

On Tue, 2005-03-01 at 20:36 +0530, Gaurav Porwal wrote:
> Hi,
> 
> Sometimes during an energy minimization using "steep" for a random
> conformation, the Potential Energy suddenly goes down to the order of
> -1.00e+16 and force becomes "inf".
If you have random conf. you may put a H on an O and there is no
repulsion between the two, just attraction.
> 
> Is this due to some kind of knot formation / cross over of loops? I can't
> find any knots as such in the structure being energy minimized.
> 
> Kindly help.
> 
> Regards,
> Gaurav
> 
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>                                                           -- Anonymous
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> 
>                            Gaurav Porwal
> 		    Senior Undergraduate Student
>  		  Department of Chemical Engineering
>                          IIT Bombay, Powai
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> 
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> 
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> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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