Hi,
what's your aim of using multihist?
I think it onlys works with 1D dataset, not with a trajectory.
Hai
On Fri, Aug 26, 2016 at 8:26 AM, Damiano Spadoni <enxds6.nottingham.ac.uk>
wrote:
> Dear Amber users,
>
> I am trying to analyse the solvation shells of a metal cluster buried in
> my protein (:1639) using a solvent mask that relates to free oxygen
> molecules (:OXY) rather than water ones. The simulation produced is about
> the solvated protein with a specific number of oxygen molecules free to
> move inside the whole system.
> This is the script I feed to cpptraj on ambertools16:
>
> parm SAMoy_noWatIons.prmtop
> trajin SAMoxy_50nsReimagedNowatIons.nc
> watershell :1639 W1_clust1.dat W1 :OXY
> multihist W1[*] out W1.hist.gnu bins 100
>
> The trajectories have been stripped from water and counterions and been
> reimaged.
> The problem I am experiencing is with the hist/multihist (I used both, but
> the results doesn't change) command that seems to be unable to produce any
> meaningful output files (loads of 0s in them).
> Visible warnings are:
>
> 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.
> 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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Received on Fri Aug 26 2016 - 11:00:02 PDT
