Hi,
On Fri, Aug 26, 2016 at 8:26 AM, Damiano Spadoni
<enxds6.nottingham.ac.uk> wrote:
> ANALYSIS: Performing 1 analyses:
> 0: [multihist W1[*] out W1.hist.gnu bins 100]
> Calculating step from min=0 max=1 bins=100.
> Dim W1[lower]: 0.000000->1.000000, step 0.010000, 100 bins.
Since you did not specify a min or max for your histogram they are
automatically determined from your data set. The apparent range for
each is 0-1, and since the 'watershell' command counts number of
molecules this means that each data set contains either 0 or 1. The
way that histograms are calculated in cpptraj are 'min <= value <
max', so the max of '1' cannot actually be binned in this case. To bin
it you'd need a max that was just above 1.0 (1.00001 etc).
That said, given that your data sets only have values of 0 or 1
(indicating that at most only 1 OXY is in the vicinity of residue 1639
over the course of this trajectory) it doesn't seem like a histogram
will tell you much in this case.
Hope this helps,
-Dan
> Hist: 25000 data points in each dimension.
> Hist: Allocating histogram, total bins = 100
> Warning: Frame 12506 Coordinates out of bounds (100)
> Warning: Frame 18054 Coordinates out of bounds (100)
> Warning: Frame 18066 Coordinates out of bounds (100)
> Warning: Frame 18069 Coordinates out of bounds (100)
> Warning: Frame 18071 Coordinates out of bounds (100)
> Warning: Frame 18072 Coordinates out of bounds (100)
> Warning: Frame 18078 Coordinates out of bounds (100)
> Warning: Frame 18082 Coordinates out of bounds (100)
> Calculating step from min=0 max=1 bins=100.
> Dim W1[upper]: 0.000000->1.000000, step 0.010000, 100 bins.
> Hist: 25000 data points in each dimension.
> Hist: Allocating histogram, total bins = 100
> Warning: Frame 12504 Coordinates out of bounds (100)
> Warning: Frame 12506 Coordinates out of bounds (100)
> Warning: Frame 12507 Coordinates out of bounds (100)
> Warning: Frame 12508 Coordinates out of bounds (100)
>
> ..and many others like those.
> My questions are: am I doing an incorrect use of multihist command? Is it a so transcendental thing using a different solvent mask for something that is not water?
> Any other has seen such warnings?
>
> Any suggestions will obviously be appreciated.
>
> Best regards,
>
> Damiano
>
>
>
>
>
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
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Received on Fri Aug 26 2016 - 11:30:02 PDT
