[gmx-users] What is the purpose that we make the bond constraints?
David van der Spoel
spoel at xray.bmc.uu.se
Fri May 22 16:38:04 CEST 2009
Chih-Ying Lin wrote:
> 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.
> 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
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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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