Subject: Averaging question....

From: "G. Ravishanker" <[email-masked]>
Date: Tue, 7 Dec 1993 14:33:53 -0500

Hi

        I have a question regarding averaging properties over an MD run -
especially those that fluctuate a lot (specifically interproton distances
in MD simulations).

        For example, if one is monitoring interproton distances for NMR
calculations, typically there is a cutoff associated with it, so that we
do not keep information on an unusual number of "unwanted" pairs. The
question is, if the cutoff is 10A and during the course of the MD, the
molecule distorted so that some pairs that did not qualify initially are
within 10A. How does (or should) one deal with this?

        1. Use a large enough cutoff that this would not matter. (The
           programs will be larger and the problem to sort things out
           will get worse).

        2. Update the interproton pairlist once every N steps.

        I prefer the second one. However, how does one average in the
second case. Let us say, there is a pair that came within 10A in the last
10 ps of a 100ps trajectory. Do I use the average distance to be 

        1. sum of distances / 10ps 

                or 

        2. sum of distances / 100ps

        Any comments or helpful insight will be appreciated.

Ravi

****************************************************************************
* Ganesan Ravishanker			Ph: (203) 344-8544 Ext. 3110       *
* Coordinator of Scientific Computing,  Fax:(203) 344-7960                 *
* Adjunct Associate Professor(Dept. of Chem.)                              *
* Wesleyan University               e-mail:[email-masked]  *
* Middletown, CT 06457.                                                    *
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