Dear all
I have successfully ran simulations for thermodynamic integration using
AMBER20.
However, when I try to run analysis, I get the following errors
/home/eph/.local/lib/python3.8/site-packages/pymbar/bar.py:467:
RuntimeWarning: divide by zero encountered in log
log_fF = - np.log(np.exp(-max_arg_F) + np.exp(exp_arg_F - max_arg_F))
/home/eph/.local/lib/python3.8/site-packages/pymbar/utils.py:324:
RuntimeWarning: overflow encountered in exp
out = np.log(np.sum(np.exp(a - a_max), axis=axis))
/home/eph/.local/lib/python3.8/site-packages/numpy/core/fromnumeric.py:87:
RuntimeWarning: overflow encountered in reduce
return ufunc.reduce(obj, axis, dtype, out, **passkwargs)
/home/eph/.local/lib/python3.8/site-packages/pymbar/bar.py:482:
RuntimeWarning: invalid value encountered in double_scalars
variance = (afF2/afF**2)/T_F + (afR2/afR**2)/T_R - nrat
Could not calculate overlap matrix
(/usr/share/texlive/texmf-dist/tex/latex/txfonts/t1txss.fd)
Class achemso Warning: No affiliations: at least one affiliation is needed on i
nput line 43.
Class achemso Warning: No e-mail given:
(achemso) at lest one author must have a contact e-mail on input l
ine 43.
(/usr/share/texlive/texmf-dist/tex/latex/txfonts/ot1txr.fd)
(/usr/share/texlive/texmf-dist/tex/latex/txfonts/utxmia.fd)
(/usr/share/texlive/texmf-dist/tex/latex/txfonts/utxsya.fd)
(/usr/share/texlive/texmf-dist/tex/latex/txfonts/utxsyb.fd)
(/usr/share/texlive/texmf-dist/tex/latex/txfonts/utxsyc.fd) (./Main.lof)
(./Main.lot) [1] [2] <LIG.bio-ref.GvsT.eps>)
*
Can you please assist to troubleshoot this?
Thank you in advance.
Regards.
Ephraim Marondedze
Computational Chemistry PhD
University of Johannesburg
Faculty of Science
Department of Chemical Sciences
+27 73 088 1526
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https://www.scopus.com/authid/detail.uri?authorId=57211852395> |
Scholar <
https://scholar.google.com/citations?user=z-YbvykAAAAJ&hl=en> |
ResearchGate <
https://www.researchgate.net/profile/Ephraim_Marondedze>
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Received on Sat Jun 26 2021 - 04:30:03 PDT
