Hi Zhen,
I would be very surprised if the dipole printing works with Amoeba. It was
designed for use with the FF02 type polarizable force fields. The Amoeba
implementation almost certainly uses different arrays for the dipoles.
Unfortunately I don't have the time to look into this right now but feel
free to dig into the code and email me if you have questions about it. It
may be possible to get it to work with Amoeba but this is probably something
Tom Darden could do a lot quicker than I.
All the best
Ross
> -----Original Message-----
> From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf
> Of Zhao, Zhen (zhaozh)
> Sent: Tuesday, October 14, 2008 10:26 AM
> To: amber.scripps.edu
> Subject: AMBER: Amber dipole printout.
>
> Hi, all
>
> I have run a simulation with the AMOEBA force field with a chloride ion
> in bulk water. I print out the induced dipole by specifying
> a dipole section at the end of the input file as the following:
>
> &dipoles
> Chloride
> ATOM 646
> END
> END
> /
> GROUPS
> END
> END
>
> The induced dipole of the chloride ion is around 5 debyes in the output
> file, which is far beyond the expected value(should not exceed 1 Debye, I
> think). I donot know if anything wrong in the code or the way I set up.
> Thanks in advance for your help!
>
> Sincerely
>
> Zhen
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Received on Wed Oct 15 2008 - 05:11:33 PDT
