[gmx-users] Average data files with gmx analyze
jalemkul at vt.edu
Wed Nov 29 14:33:42 CET 2017
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..."
> 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.
You cannot pass multiple files to gmx analyze via -f, and certainly not
> (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
> + Hecho gmx analyze -f den1.xvg
Justin A. Lemkul, Ph.D.
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
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