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From: Dmitry Mukha <dvmukha.gmail.com>

Date: Sat, 25 Aug 2012 18:59:06 +0300

Hi All,

2012/8/23 Daniel Roe <daniel.r.roe.gmail.com>:

*> Hi,
*

*>
*

*> >
*

*> More specifically, in the "<file>_a.xmgr" file the second column is
*

*> the average distance travelled by all the atoms, i.e. sqrt(
*

*> SUM[dist^2]/N ), where N is the number of atoms. Columns 3 and 4 in
*

Actually, you are not right. sqrt(SUM[dist^2]/N )>=SUM[dist]/N, and a

case of equality appears when 'dist'=const.

In general form, for large numbers, mean square = square of mean + variance

2Bala:

If you use 'average' key word, you will get only 2 columns, one for

time and one for the appropriate mean value.

_r - mean square displacement,

_a - mean displacement,

_x, _y, _z - Cartesian decomposition.

*> this case are the distance travelled by each individual atom, i.e.
*

*> sqrt( dist^2 ), so col2 should not be equal to the straight average of
*

*> cols 3 and 4, but rather col2 = sqrt( (col3^2 + col4^2) / 2), which
*

*> you can verify it is.
*

*>
*

*> Hope this helped.
*

*>
*

*> -Dan
*

*>
*

*> --
*

Date: Sat, 25 Aug 2012 18:59:06 +0300

Hi All,

2012/8/23 Daniel Roe <daniel.r.roe.gmail.com>:

Actually, you are not right. sqrt(SUM[dist^2]/N )>=SUM[dist]/N, and a

case of equality appears when 'dist'=const.

In general form, for large numbers, mean square = square of mean + variance

2Bala:

If you use 'average' key word, you will get only 2 columns, one for

time and one for the appropriate mean value.

_r - mean square displacement,

_a - mean displacement,

_x, _y, _z - Cartesian decomposition.

-- Sincerely, Dmitry Mukha Institute of Bioorganic Chemistry, NAS, Minsk, Belarus _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Sat Aug 25 2012 - 09:00:02 PDT

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