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 <[EMAIL PROTECTED]
<mailto:[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
>
>
>
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________________________________________________________________________
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]
<mailto:[EMAIL PROTECTED]> [EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]> 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
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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