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

[David van der Spoel]

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?

chapter 1.


> What is the purpose that we make the bond constraints?
> I read the manual but could not answer the question by myself.
> 
> 
> 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
> 
> 
> Thank you
> Lin
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Professor of Biology
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://folding.bmc.uu.se
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