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.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
>
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Received on Wed Jul 06 2005 - 16:53:00 PDT
