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 - 03:00:03 PDT
