Hi,
RMS fitting coordinates with periodic boundary conditions directly does not
work because although the coordinates are rotated, the unit cell is not.
Your best bet is to RMS fit, strip out solvent, save as PDB or mol2, then
resolvate with the same number of waters.
Hope this helps.
-Dan
On Wednesday, May 22, 2013, kurisaki wrote:
> Dear Amber developers and users,
>
> I use sander to (re)calculate energy and force
> from an obtained MD trajectory by setting "imin = 5".
>
> There, I found that a MD trajectory which was preliminarily RMSd-fit on a
> coordinates
> shows "blow-up" of energy and force.
> I guess that due to usage of PME...but it still remains unclear for me.
>
> I am grateful if you give an answer for this question
> and let me know how to avoid it after RMS-fit for MD trajectory, if
> possible.
>
> Yours sincerely,
>
> Ikuo KURISAKI
>
>
>
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Wed May 22 2013 - 06:00:08 PDT
