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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--
========================================
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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