[gmx-users] Question about angle constraints

[David van der Spoel]

Qiao Baofu wrote:
> 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.


this may work, just try it. However, be careful that the number of 
degrees of freedom is correct, that is it won't be correct! You will 
have to adapt the temperature in your simulation to match it.

> 
> *********** .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
Typo on the above line...

>     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 
> <mailto: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
>     <mailto:spoel at xray.bmc.uu.se>    spoel at gromacs.org
>     <mailto:spoel at gromacs.org>   http://folding.bmc.uu.se
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> 
> 
> 
> -- 
> 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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