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From: Daniel Roe <daniel.r.roe.gmail.com>

Date: Thu, 23 Aug 2012 13:09:58 -0600

Hi,

On Thu, Aug 23, 2012 at 8:41 AM, Bala subramanian

<bala.biophysics.gmail.com> wrote:

*> If I understand well, col 2 is the average msd of the two atoms, col 3
*

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

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: Thu, 23 Aug 2012 13:09:58 -0600

Hi,

On Thu, Aug 23, 2012 at 8:41 AM, Bala subramanian

<bala.biophysics.gmail.com> wrote:

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

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

-- ------------------------- 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) _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Thu Aug 23 2012 - 12:30:03 PDT

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