[gmx-users] Question about angle constraints

[David van der Spoel]

Qiao Baofu wrote:
> Hi All,
> 
> In my simulation, the NO3- is used, in which the three N-O bond length 
> is constraints. And a planar triangular structure is used.
> I used the type "1" of [ constraints ] to constraint the bond length. 
> Because I only find angle constraints which is used on H-involved angles,
> I used the type "2" of [ constraints ] to constraint the length between 
> Os.  (The distance is calculated from the triangular structure). After 
> the Energy Minimization, all the bong length become very long (much 
> bigger than the box length).   Who knows how to solve it?
> 

You probably have an error in the topology. Check energy terms.

However, you probably should consider modeling this using either an 
improper dihedral to keep the N in the plane or, if you want to keep the 
molecule planar at every time use a virtual site representation for the N.

> Sincerely yours,
> Baofu Qiao, PhD
> 
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
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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