[gmx-users] Average data files with gmx analyze

[Justin Lemkul]

On 11/29/17 4:35 AM, mario at exactas.unlpam.edu.ar wrote:
> Dear GROMACS developers:
> The gmx tutorial tells me that in order to average data from columns of
> several similar files XVG, I must use gmx analize
> "gmx analyze reads an ASCII file and analyzes data sets. ... Multiple sets
> can also be read when they are separated by & (option -n); in this case
> only one y-value is read from each line..."
> (http://manual.gromacs.org/programs/gmx-analyze.html)
>
> But the indication does not seem clear.
>
> I try to average data from den1.xvg, den2.xvg etc files
>
> I already tried, among other things, this sequence of indications and it
> does not work:
> gmx analyze -f den1.xvg & den2.xvg -n 2 -av
>
> Could you tell me what I'm doing wrong?

The description refers to multiple data sets in a single file, separated 
by &, as is produced by several GROMACS programs.

@set1
x1 y1
x2 y2
...
&
@set2
x1 y1
x2 y2
...

You cannot pass multiple files to gmx analyze via -f, and certainly not 
with &.

-Justin

> (I add the answer in terminal (summarized)):
>
> GROMACS:      gmx analyze, VERSION 5.1.2
> Executable:   /usr/bin/gmx
> Data prefix:  /usr
> Command line:
>    gmx analyze -f den1.xvg
>
> Read 1 sets of 5001 points, dt = 2
>
>                                        std. dev.    relative deviation of
>                         standard       ---------   cumulants from those of
> set      average       deviation      sqrt(n-1)   a Gaussian distribition
>                                                        cum. 3   cum. 4
> SS1   1.683733e+01   1.830422e-01   2.588608e-03       0.047   -0.045
>
>
> gcq#433: "If you want to save your child from polio, you can pray or you
> can inoculate... choose science." (Carl Sagan)
>
> den2.xvg: no se encontró la orden
> [1]+  Hecho                   gmx analyze -f den1.xvg
>
>
>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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jalemkul at vt.edu | (540) 231-3129
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