[gmx-users] Average data files with gmx analyze

[mario at exactas.unlpam.edu.ar]

Dear Justin:
thank you very much!
best regards!
Mario Campo

>
>
> 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
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==================================================
>
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