[gmx-users] correlation function

[Mark Abraham]

Jamie Seyed wrote:
> Hi Mark,
> Thanks for the information. Actually in 7.4 I found only g_rotacf and
> g_angle also g_sgangle that calculate rotation and angle correlation
> function and in appendix D I could not find related topic... I appreciate if
> someone gives me more detail to do the job.
> I want to calculate <R(0).R(t)> that R is coordinates vector R(x,y,z) for
> pure spce water.

If that's an auto-correlation function, then g_analyze does the job. 
Searching for "correlation" in the manual was a good way to start. That 
would also have found a whole section devoted to the topic, which is 
good reading.

> Also I have a question related to having a coordinate file. I did a command
> as
> trajconv  -f  md.trr  -n f.ndx  -o md.xtc
> I am supposing in this case md.xtc contains only x,y,z coordinates. Is that
> true?? Many Thanks in Advance/Jamie

Yes, since the compression algorithm used for .xtc only works on 
positions. However it is a lossy compression, and if you want 
full-precision positions-only, look at the options in trjconv -h.

Mark