Hi David,<br><br>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.<br>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.
<br>2. Except the bond-length, the angles F-P-F should be constrainted to be 90 or 180.<br><br>*********** .itp file*********************<br>[ moleculetype ]<br>; Name PF6- <br>PFN 3<br><br>[ atoms ]<br>; nr type resnr resid atom cgnr charge mass
<br> 1 opls_977 1 PFN PAA 1 1.34 30.97376<br> 2 opls_978 1 PFN FAA1 1 -0.39 18.99840<br> 3 opls_978 1 PFN FAA2 1 -0.39 18.99840<br> 4 opls_978 1 PFN FAA3 1 -
0.39 18.99840<br> 5 opls_978 1 PFN FAA4 1 -0.39 18.99840<br> 6 opls_978 1 PFN FAA5 1 -0.39 18.99840<br> 7 opls_978 1 PFN FAA6 1 -0.39 18.99840<br><br>[ constraints ]
<br> 1 2 1 0.1560<br> 1 3 1 0.1560<br> 1 4 1 0.1560<br> 1 5 1 0.1560<br> 1 6 1 0.1560<br> 1 7 1 0.1560<br><br>; The structure of PF6- is Octahedral<br>[ constraints ]
<br> 2 3 2 0.2206<br> 2 4 2 0.2206<br> 2 5 2 0.3120<br> 2 6 2 0.2206<br> 2 7 2 0.2206<br> 3 4 2 0.2206<br> 3 5 2 0.2206<br> 3 6 2 0.3120<br> 3 7 2
0.2206<br> 4 5 2 0.2206<br> 4 6 2 0.2206<br> 4 7 2 0.3120<br> 5 6 2 0.2206 <br> 5 7 2 0.2206 <br> 6 7 2 0.2206 <br><br>******************* .top file******************
<br>;the force field files to be included<br>#include "ffoplsaa.itp"<br><br><br>; include the PF6- topology<br>#include "PFN.itp"<br><br>[ system ]<br>PFN<br><br>[ molecules ]<br>; molecule name number
<br> PFN 5<br>****************************************<br><br><br><div><span class="gmail_quote">2006/8/30, David van der Spoel <<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a>>:</span>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">Qiao Baofu wrote:<br>> Hi All,<br>><br>> In my simulation, the NO3- is used, in which the three N-O bond length
<br>> is constraints. And a planar triangular structure is used.<br>> I used the type "1" of [ constraints ] to constraint the bond length.<br>> Because I only find angle constraints which is used on H-involved angles,
<br>> I used the type "2" of [ constraints ] to constraint the length between<br>> Os. (The distance is calculated from the triangular structure). After<br>> the Energy Minimization, all the bong length become very long (much
<br>> bigger than the box length). Who knows how to solve it?<br>><br><br>You probably have an error in the topology. Check energy terms.<br><br>However, you probably should consider modeling this using either an<br>
improper dihedral to keep the N in the plane or, if you want to keep the<br>molecule planar at every time use a virtual site representation for the N.<br><br>> Sincerely yours,<br>> Baofu Qiao, PhD<br>><br>><br>
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<br>--<br>David.<br>________________________________________________________________________<br>David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,<br>Dept. of Cell and Molecular Biology, Uppsala University.
<br>Husargatan 3, Box 596, 75124 Uppsala, Sweden<br>phone: 46 18 471 4205 fax: 46 18 511 755<br><a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a> <a href="mailto:spoel@gromacs.org">spoel@gromacs.org
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</a><br></blockquote></div><br><br clear="all"><br>-- <br>Sincerely yours,<br>Baofu Qiao, PhD<br>