[gmx-users] coinstraint bond length changes

[Justin A. Lemkul]

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  

-- 
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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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