Hi,
On Thursday, 29. May 2008 13:03, Thomas Leonard wrote:
> Hi,
>
> Why unusual bonds are formed during minimization.
>
> In my case I have problem with unusual bond formation (which is not
> expected) at the nitrogen,oxygen of FADH cofactor
in normal MD simulation no bond breaking can occur.
Your question is not clear to me, I think you have done following:
If you calculate an average structure of your simulation and than view it as a
pdb file, than you can see "unphysical bonds".
Easy solution is to minimize this average structure.
>
> Thomas
>
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Greetings,
Florian
--
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Florian Haberl
Computer-Chemie-Centrum
Universitaet Erlangen/ Nuernberg
Naegelsbachstr 25
D-91052 Erlangen
Telephone: +49(0) − 9131 − 85 26573
Mailto: florian.haberl AT chemie.uni-erlangen.de
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Received on Sun Jun 01 2008 - 06:07:30 PDT
