[CPMD-list] How to make a bond broken by force?

[Axel Kohlmeyer]

On Wed, 21 Dec 2005, Yang Zhenyu wrote:

YZ>  Dear CPMD users:

dear yang zhenyu,

YZ> 	 I meet a tough problem. I want to know how much forces needed
YZ> to broken a covalent bond by CPMD(actually,I don't whether CPMD can

note, that since CPMD uses quantum mechanics (DFT to be more exact) 
to determine the electron structure, which is responsible for the 
bonding, it has no concept of covalent or other types of bonds by
itself. the DFT calculation just basically tells how high the potential
energy and the resulting forces are for a given arrangement of atoms.

YZ> solve this problem). So I imagine that one atom is fixed and I move

yes, it can. there are actually two quantities, that you can calculate.

YZ> the other atom along the bond by a small step, then constrain it.
YZ> Now I can calculate the force on the constraint(is this right?). And
YZ> I move the atom step by step until the bond broken, maybe I can get
YZ> a max force which is considered as the force breaking the bond. Is
YZ> this a right way to solve it?

i assume, that you want to do this during an MD run, right? then what
you describe is a technique called umbrella sampling: in your case you
would put a distance constraint on your bond and then do an MD for a
certain time. CPMD will write the contraint force automatically into a
file called CONSTRAINT and you just have to take the average of that
(the MD of course has to be long enough so the force is converged). now
you change the constraint a bit and repeat. this way you will get the
potential of mean force and by integrating it numerically, you'd get the
free energy barrier for breaking this bond. there are some references
about this given in the constraints section of the cpmd manual. also a
look in any textbook on molecular dynamics should help.

btw.: an alternative, less obvious way could be to use the metadynamics 
module to determine the free energy profile and then just take the 
(numerical) derivative to get the PMF.

regards,
      axel.

YZ>  
YZ>      Any suggestions will be appreciated!
YZ> 
YZ>  				
YZ> 
YZ> ¡¡¡¡¡¡¡¡¡¡¡¡¡¡
YZ> ¡¡Best Regards
YZ> 
YZ> ¡¡Yang Zhenyu				
YZ>   State Key Laboratory of Nonlinear Mechanics (LNM)
YZ>   Institute of Mechanics, Chinese Academy of Sciences
YZ>   No.15 Beisihuanxi Road
YZ>   Beijing 100080, P. R. China
YZ>   FAX: 010-62579511
YZ> ¡¡yangzy at lnm.imech.ac.cn
YZ> ¡¡2005-12-21
YZ> 
YZ> 
YZ> _______________________________________________
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YZ> 

-- 
=======================================================================
Axel Kohlmeyer   akohlmey at cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
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