Hello,
I can't speak to the anharmonicity error, but the "index 516 is out of
bounds..." error is most likely because your weights list and your reaction
coordinates list are different sizes. Do your 2.dat and weights.dat file
have the same amount of lines? Perhaps you could be including the
coordinates from the preliminary GaMD biasing steps in your 2.dat file.
I believe the c1, c2, and c3 are cumulant expansion to the first order,
second order, and third order. According to the Miao lab guide on
reweighting (
https://www.med.unc.edu/pharm/miaolab/resources/pyreweighting/)
the second order usually gives the best result.
Hope this helps :)
Skanda
On Thursday, November 2, 2023, Munazzah Fatima Ansari via AMBER <
amber.ambermd.org> wrote:
> Hello developers,
>
> I am running the GaMD. But when I am doing re-weighting and calculate
> the anharmonicity with reaction coordinates RMSD and ROG. It gives me
> the following error:
>
> ERROR DURING REWEIGHTING:
> Traceback (most recent call last):
> File "/home/vector/PyReweighting-2D.py", line 544, in <module>
> main()
> File "/home/vector/PyReweighting-2D.py", line 139, in main
> hist2,newedgesX,newedgesY,binfX,binfY,dV_avg,dV_std,dV_anharm,dV_mat
> = reweight_dV(inputfile,hist_min,binsX,binsY,discX,discY,dV,T)
> File "/home/vector/PyReweighting-2D.py", line 417, in reweight_dV
> dV_mat[jx,jy,int(nA[jx,jy])] = dV[i]
> IndexError: index 516 is out of bounds for axis 2 with size 516
>
> ERROR DURING ANHARMONICITY :
> main()
> File "/home/vector/PyReweighting-2D.py", line 118, in main
> hist2=prephist(hist2,T,cb_max)
> File "/home/vector/PyReweighting-2D.py", line 294, in prephist
> hist2=np.max(hist2)-hist2 ## zero value to lowest energy state
> File "<__array_function__ internals>", line 5, in amax
> File
> "/apps/anaconda3/lib/python3.9/site-packages/numpy/core/fromnumeric.py",
> line 2754, in amax
> return _wrapreduction(a, np.maximum, 'max', axis, None, out,
> File
> "/apps/anaconda3/lib/python3.9/site-packages/numpy/core/fromnumeric.py",
> line 86, in _wrapreduction
> return ufunc.reduce(obj, axis, dtype, out, **passkwargs)
> ValueError: zero-size array to reduction operation maximum which has no
> identity
>
> I use the following command to calculate the re-weighting and
> anharmonicity :
>
> python PyReweighting-2D.py -cutoff 8 -input 2.dat -Xdim 5 17 -discX 0.2
> -Ydim 0 30 -discY 0.2 -Emax 20 -job amdweights_CE -weight weights.dat |
> tee -a reweight_variable.log
>
> python PyReweighting-2D.py -cutoff 8 -input 2.dat -Xdim 5 17 -discX 0.2
> -Ydim 0 30 -discY 0.2 -Emax 20 -job amd_dV -weight weights.dat | tee -a
> reweight_variable.log
>
> I also want to ask for the three files in output after re-weighting
> pmf-c1-2.dat.xvg , pmf-c2-2.dat.xvg ,pmf-c3-2.dat.xvg. what is the
> difference between these files? What C1, C2, C3 refers to ?
> Thanks in Advance
>
> Munazzah
> Ph.D Scholar
> RRCAT, INDORE
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Received on Thu Nov 02 2023 - 09:30:02 PDT
