AMBER Archive (2005)

Subject: Re: AMBER: how to average the structure along md trajectory

From: Angelo Pugliese (angelo_at_holmes.cancres.nottingham.ac.uk)
Date: Wed Jul 06 2005 - 10:02:48 CDT

Hi,

You may minimise (optimise) the average structure...have a go.

Angelo

Ye Mei wrote:

> Dear amber users£¬
>
> I wanna try to average the md trajectory and compare it with x-ray crystal structure. I tried average keyword in ptraj module. But the averaged structure has shorter bond length. This can be explained if one tries to average the structure by cartesian coordinates. For example, the average structure of spinning water molecule in only one point. Is there anyway to average the trajectory but keep the bond length?
> ¡¡¡¡¡¡¡¡¡¡¡¡
>
> Best regards,
>
> Ye Mei
> ymei_at_itcc.nju.edu.cn
> Institute of Theoretical and Computational Chemistry
> Key Laboratory of Mesoscopic Chemistry
> School of Chemistry and Chemical Engineering
> Nanjing University
> Nanjing 210093
> P.R.China
> 2005-07-06
>
> -----------------------------------------------------------------------
> 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