[gmx-users] bond constraint

Justin A. Lemkul jalemkul at vt.edu
Fri Jun 19 20:54:23 CEST 2009

noob noob wrote:
> Dear all,.
> I am quite new in MD simulations. I am planning to learn some simple 
> simulation, and now i encounter a little doubt about the bond 
> constraint. I get many references and papers to design a method for my 
> simulation but I cannot get a reference that use "no bond constraint" in 
> their works. 
> Hence, my question is:
> Is it possible if we do not use bond constraint in our system?

Yes.  You can set "constraints = none" in the .mdp file.

> What is the different or effect if we do not use bond constraint compare 
> to those are using  "all-bond "bond constraint?
> is it wrong if we do not use bond constraint in our system?

It is not wrong, but it is quite advantageous to use constraints.  If you don't, 
you have to use a much smaller timestep and verify that energy is properly 
conserved.  Refer to the LINCS and P-LINCS papers (cited in the manual), and the 
references therein.


> Thanks for any suggestions.
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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