AMBER Archive (2006)

Subject: Re: AMBER: Ptraj: radial distribution and correlation coefficient

From: Austin B. Yongye (ayongye_at_chem.uga.edu)
Date: Tue Nov 14 2006 - 12:50:01 CST

Thanks for the response.
austn-

>
>> I am using ptraj to calculate some radial pair distributions between
>>
>> It seems the second column represents rpd values. Would be glad to know
>> what the third column stands for?
>
> The integrated value (occupancy).
>
>> I am also calculating correlation coefficients from the same trajectory.
>> Here is my input file:
>>
>> trajin md.crd
>> vector vec :1-3 dipole
>> analyze correlationcoefficient {vec | ALL}
>
> That syntax means specify a vector name or ALL, so
>
> analyze correlationcoefficient ALL
>
> or
>
> analyze correlationcoefficient vec
>
>
> --tec3_at_utah.edu
>
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