[gmx-users] Question about angle constraints

David van der Spoel spoel at xray.bmc.uu.se
Wed Aug 30 17:01:24 CEST 2006

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
> ------------------------------------------------------------------------
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

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

More information about the gromacs.org_gmx-users mailing list