On Wed, May 30, 2007, lishan yao wrote:
> I am running MD simulation for a small protein with explicit water. I
> want to find out the electric field on each backbone Nitrogen atom. Is there
> a way to do it?(My speculation is that it may not work with PME method
> switch on in my simulation).
>
This is not printed out in the current code, so you will have to extract
the total electrostatic force on each nitrogen, then divide by the nitrogen
partial charge. Be aware that molecular mechanics force fields skip 1-2 and
1-3 electrostatic interactions, so you may need to think about how to
compensate for this.
Since we are doing some similar things, this facility may be incorporated into
the next release of Amber (I know: not much help for now!)
....dac
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Received on Sun Jun 03 2007 - 06:07:17 PDT
