[gmx-users] What is the purpose that we make the bond constraints?

[Justin A. Lemkul]

Chih-Ying Lin wrote:
> Hi
> All atoms are connected by the covalent bonds and all atoms are
> constrainted by the force field.
> 
> Why do we need the bond constraints?
> What is the purpose that we make the bond constraints?
> I read the manual but could not answer the question by myself.
> 

References 33 and 34 in the manual (for LINCS and P-LINCS, respectively) are 
instructive.  As a matter of fact, within the first two sentences of the LINCS 
paper, the advantages of constraints are explicitly stated.

> 
> How do the following parameters work?
> ; OPTIONS FOR BONDS
> constraints              = all-bonds
> constraint-algorithm     = Lincs
> unconstrained-start      = yes
> lincs-order              = 4
> lincs-iter               = 1
> lincs-warnangle          = 30
> 

The manual has complete descriptions of each of these parameters - section 7.3.18.

-Justin

> 
> Thank you
> Lin
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-- 
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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
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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