[gmx-users] Question about angle constraints

[Qiao Baofu]

Hi David,

I think maybe the virtual site is suitable for NO3-. But how about PF6-?
Please see the .itp file for the PF6-, which is wroten by myself.
1. Because all the bond-length are constrainted,  there is no energy term in
the .itp file. Therefore it is not a problem of energy term, I think.
2. Except the bond-length, the angles F-P-F should be constrainted to be 90
or 180.

*********** .itp file*********************
[ moleculetype ]
; Name PF6-
PFN      3

[ atoms ]
;   nr    type    resnr   resid   atom  cgnr  charge    mass
    1    opls_977     1    PFN    PAA    1    1.34   30.97376
    2    opls_978     1    PFN   FAA1    1   -0.39   18.99840
    3    opls_978     1    PFN   FAA2    1   -0.39   18.99840
    4    opls_978     1    PFN   FAA3    1   -0.39   18.99840
    5    opls_978     1    PFN   FAA4    1   -0.39   18.99840
    6    opls_978     1    PFN   FAA5    1   -0.39   18.99840
    7    opls_978     1    PFN   FAA6    1   -0.39   18.99840

[ constraints ]
  1   2    1     0.1560
  1   3    1     0.1560
  1   4    1     0.1560
  1   5    1     0.1560
  1   6    1     0.1560
  1   7    1     0.1560

; The structure of PF6- is Octahedral
[ constraints ]
  2   3    2     0.2206
  2   4    2     0.2206
  2   5    2     0.3120
  2   6    2     0.2206
  2   7    2     0.2206
  3   4    2     0.2206
  3   5    2     0.2206
  3   6    2     0.3120
  3   7    2     0.2206
  4   5    2     0.2206
  4   6    2     0.2206
  4   7    2     0.3120
  5   6    2     0.2206
  5   7    2     0.2206
  6   7    2     0.2206

******************* .top file******************
;the force field files to be included
#include "ffoplsaa.itp"


; include the PF6- topology
#include "PFN.itp"

[ system ]
PFN

[ molecules ]
; molecule name   number
  PFN               5
****************************************


2006/8/30, David van der Spoel <spoel at xray.bmc.uu.se>:
>
> 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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-- 
Sincerely yours,
Baofu Qiao, PhD
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