On Fri, Dec 13, 2013, 张明焜 wrote:
>
> I want to remove all the translational and rotational
> center-of-mass motion in a MDCRD file.For translational center-of-mass
> motion,I konw I can handle it with the command "center" in Ptraj, but is
> there any command to deal with the rotational center-of-mass motion in
> AMBER ?
Well, technically, the center of mass is a point and does not have rotational
motion. So you have to find some way to define internal axes in your
molecule, and for a flexible molecules you have various options. By far the
most common choice is to do an rms fit to some reference structure.
See the "rms" command in ptraj.
...dac
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Received on Fri Dec 13 2013 - 05:00:02 PST
