Sebastian Waltz wrote:
Hi all,
I constrained in the .top file some bonds
[ constraints ]
;ai aj type distance
40 41 2 0.1430
47 48 2 0.1430
54 55 2 0.1430
61 62 2 0.1430
After running the simulation for 5ns I get a bond length of
0.23....(out of the .trr file). So I am not sure whats
going wrong. This bonds are C O double bonds which have an
equilibrium bond length of 0.143nm.
Since these are actual chemical bonds, why are you using constraint type 2
instead of 1? See the manual, section 5.4 regarding the proper function type.
-Justin
Thanks a lot
Sebastian
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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