AMBER Archive (2006)

Subject: Re: AMBER: offset?

From: Angelo (angelo_at_holmes.cancres.nottingham.ac.uk)
Date: Thu Jun 01 2006 - 04:39:20 CDT

Hi,

For instance if the offset is equal to 2, ptraj to produce the average
structure will not consider all the coordinate sets (frames) from your
trajectories but just one coordinate set every 2 coordinate sets.

If you have 10 coordinate sets in your trajectories, ptraj will read and
use to calculate the average structure only 5 of them.

hope it helps

Angelo

Tonda March wrote:

> Dear AMBER community,
>
> I am new to using ptraj and I have a question about one of the
> keywords. When using the command "average" in ptraj, what exactly is
> the meaning of the "offset" term? The command allows you to set
> "start", "stop", and "offset" for the configurations read in, and I
> don't understand what "offset" means in this context.
>
> Apologies for asking such a basic question. Thank you very much in
> advance for any advice.
>
> -Tonda
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
>

This message has been checked for viruses but the contents of an attachment
may still contain software viruses, which could damage your computer system:
you are advised to perform your own checks. Email communications with the
University of Nottingham may be monitored as permitted by UK legislation.

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu