You should check any regular text book on classical molecular dynamics for
the answer to this question. Consider the equation used for the bond energy.
If you want to study bond breaking or formation you will have to look into
QMMM techniques.
All the best
Ross
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|\oss Walker
| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
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> -----Original Message-----
> From: owner-amber.scripps.edu
> [mailto:owner-amber.scripps.edu] On Behalf Of vannajan.chiangmai.ac.th
> Sent: Tuesday, August 02, 2005 19:11
> To: amber.scripps.edu
> Subject: AMBER: bond breaking/ energetic ion
>
> Dear friends;
> I've tried to observed the interactions between accelerated
> Fe2+ to the
> cellulose wall by modifying the nonbonded parameter and the
> velocity for
> Fe2+ in file Fe.lib, using the param99 force field for
> cellulose with no
> boundary condition. However, I found that no matter how much
> energy that I
> increase (in my case the velocity in only Z direction was
> changed (eg. 0
> 0 60000)), I am not able to break any bond in the cellulose. There
> should be some bond breaking and some fragments after the
> hit. Can Amber
> do the bond breaking simulation?
> Thank you very much,
> Vanna
> --
> Vannajan Sanghiran, Ph.D
> Deparment of Chemistry,
> Faculty of Science,
> Chiang Mai University,
> Chiang Mai, Thailand 50200
> Tel: 66-53-943341 ext. 117
> Fax: 66-53-892277
>
> --------------------------------------------------------------
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>
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Received on Wed Aug 03 2005 - 03:53:00 PDT
