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

Date: Thu, 9 Jan 2014 15:55:41 -0700

Hi,

You can calculate the auto-correlation function of a data set (or

cross-correlation of 2 data sets) in cpptraj with the 'corr' command. Note

however that 'corr' doesn't yet handle periodic data sets properly, so if

your dihedral data 'jumps' (e.g. crosses back and forth from < 180 to >

-180) the result won't be correct. If your data does jump around like this

you can try shifting it by using the the 'range360' argument of the

'dihedral' command prior to calculating the auto-correlation function. If

your data doesn't jump the calculated correlation function should be fine.

The upcoming AmberTools 14 version of cpptraj will correctly calculate

correlation functions for periodic data.

Hope this helps,

-Dan

PS - Note that by default cpptraj 'corr' really calculates covariance

(which is usually what you want) - to do a raw correlation you need to

specify 'nocovar'.

On Thu, Jan 9, 2014 at 1:02 PM, Jose Borreguero <borreguero.gmail.com>wrote:

*> Dear Amber gurus,
*

*>
*

*> I have used ptraj to output the trajectory of a particular dihedral angle
*

*> but it seems there's no utility in ptraj to calculate the autocorrelation
*

*> function. Am I missing something? Otherwise, is there a package or program
*

*> I can use straight away (I'm trying to save me some scripting time) ?
*

*>
*

*> Thanks in advance!
*

*> -Jose
*

*> _______________________________________________
*

*> AMBER mailing list
*

*> AMBER.ambermd.org
*

*> http://lists.ambermd.org/mailman/listinfo/amber
*

*>
*

Date: Thu, 9 Jan 2014 15:55:41 -0700

Hi,

You can calculate the auto-correlation function of a data set (or

cross-correlation of 2 data sets) in cpptraj with the 'corr' command. Note

however that 'corr' doesn't yet handle periodic data sets properly, so if

your dihedral data 'jumps' (e.g. crosses back and forth from < 180 to >

-180) the result won't be correct. If your data does jump around like this

you can try shifting it by using the the 'range360' argument of the

'dihedral' command prior to calculating the auto-correlation function. If

your data doesn't jump the calculated correlation function should be fine.

The upcoming AmberTools 14 version of cpptraj will correctly calculate

correlation functions for periodic data.

Hope this helps,

-Dan

PS - Note that by default cpptraj 'corr' really calculates covariance

(which is usually what you want) - to do a raw correlation you need to

specify 'nocovar'.

On Thu, Jan 9, 2014 at 1:02 PM, Jose Borreguero <borreguero.gmail.com>wrote:

-- ------------------------- 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) 585-6208 (Fax) _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Thu Jan 09 2014 - 15:00:03 PST

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