AMBER Archive (2008)

Subject: Re: AMBER: using ptraj

From: Gustavo Seabra (gustavo.seabra_at_gmail.com)
Date: Fri Oct 17 2008 - 20:35:23 CDT

Did you take a look at the 'analyze timecorr' option of ptraj? Look
into sec."10.5. Correlation and fluctuation facility" in the Manual.

Also, notice you are not bound to use this version of ptraj, even if
you only have Amber9 license. Ptraj is now part of the "AmberTools"
package, which is free and the most recent version can be downloaded
here: http://ambermd.org/#AmberTools

Gustavo.

2008/10/17 Adrien Delmont:
> Dear All,
>
> How can I evaluate velocity and time autocorrelation functions using ptraj
> in Amber 9 v. ? I couldn't get an explanation anywhere. So Could you give me
> the information about this ? And I also want to ask if the diffusion
> coefficient can be calcuated in ptraj from the integral below ?
>
> D0= $B"i(B < vi(0)vi(t) > dt
>
>
>
> Thanks in advance!
>
> Regards, Adrien
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