[gmx-users] correlation function

Jamie Seyed jamie.seyed at gmail.com
Sun Aug 23 00:07:34 CEST 2009

Hi Mark,
Thanks for the answers. I want to use g_analyze but it needs a file
graph.xvg as an input file. How can I get that for calculation
of auto-correlation function? Many Thanks in Advance/Jamie

On Fri, Aug 21, 2009 at 7:57 PM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:

> 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
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