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 <[EMAIL PROTECTED]>:
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 [email protected]
> 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 [EMAIL PROTECTED].
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
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
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
_______________________________________________
gmx-users mailing list [email protected]
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 [EMAIL PROTECTED].
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
Sincerely yours,
Baofu Qiao, PhD
_______________________________________________ gmx-users mailing list [email protected] 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
