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Conformational sampling help - geometry optimisation problems #382
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Sorry, no idea. From that description I can't see what might be going wrong here. |
I installed via conda and the version seems to be 3.0.2 on Mac. I was looking at past questions/issues and also came to the conclusion that it may be the implicit solvation. I do get trj files so i might just grab those structures and run in xTB since this runs fine but not entirely sure why crest geometry optimisation gives me issues at times even if my molecules are intact/not strained..? |
Hm, running on Mac might be an issue as well. The installation technically works, but it is not well-tested. Though, that's more of a personal feeling rather than hard evidence. |
Thanks for the reply. |
If you are talking about Ubuntu subsystem for Windows, that might work. Windows Powershell won't.
Yes, building from the master branch is recommended, conda does not automatically do that. |
Hi, |
Hi all,
I am trying to produce a conformational search on nonenolide.
I initially use xtb to geometry optimise in GFN2-xTB in using methanol alpb model
xtb nonenolide.xyz --opt -c 0 -u 0 --gfn 2 --alpb methanol bar1M --namespace nonenolide_initialOpt > nonenolide_initialOpt.log
i then proceeded to do
crest nonenolide_initialOpt.xtbopt.xyz --gfn2 --alpb methanol -T 4 -chrg 0 -uhf 0
which seems to work until the end
| Multilevel Ensemble Optimization |
Optimizing all 686 structures from file "crest_dynamics.trj" ...
crude pre-optimization
Optimization engine: ANCOPT
Hessian update type: BFGS
E/G convergence criteria: 0.500E-03 Eh, 0.100E-01 Eh/a0
maximum optimization steps: 200
[##################################################] 100.00% finished.
I looked into the crest-dynamics.trj files and the molecules do not seem broken and look fine (also they do not look that strained)
I played around (assuming my optimisation had some issues) and some errors i stumbled upon
I also tried pre-optimisation with xtb with --opt vtight and then tried the crest command above
tb nonenolide.xyz --opt vtight -c 0 -u 0 --gfn 2 --alpb methanol bar1M --namespace nonenolide_initialOpt > nonenolide_initialOpt.log crest nonenolide_initialOpt.xtbopt.xyz --gfn2 --alpb methanol -T 4 -chrg 0 -uhf 0
and got this error:
Calculation info
Initial Geometry Optimization
Geometry successfully optimized.
WARNING Change in topology detected!
Topology change compared to the input affects atoms:
1(O) 2(C) 3(H) 4(C) 5(C) 6(C) 7(H) 8(O) 9(C) 10(C) 11(C) 12(H) 13(C) 14(O) 15(C) 16(C) 17(O) 18(H) 19(H) 20(H) 21(H) 22(H) 23(H) 24(H) 25(H) 26(H) 27(H) 28(H) 29(H) 30(H)
READ THE FOLLOWING CAREFULLY
A topology change was seen in the initial geometry optimization.
This could be an artifact of the chosen theory level (e.g. xTB).
You can check the optimization trajectory in the "crestopt.log" file.
Try either of these options:
Note: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG
ERROR STOP safety termination of CREST
Based on (A) I then proceeded to attempt
crest nonenolide_initialOpt.xtbopt.xyz --opt tight -alpb methanol -gfn2 -chrg 0 -uhf 0 -T 4
which leads to a weird "successful" geometry optimisation
Calculation info
gradient norm : 0.0000243 Eh/a0 predicted 0.0000000E+00 ( -0.00%)
generating ANC from model Hessian ...
Using Lindh-Hessian (1995)
Shifting diagonal of input Hessian by 8.2450733776528520E-003
Lowest eigenvalues of input Hessian
0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
0.010000 0.010448 0.012718 0.013957 0.014477 0.016153
0.016361 0.017065 0.018196 0.018993 0.021503 0.021755
Highest eigenvalues
1.447169 1.476450 1.516883 1.846698 1.952443 2.275661
total energy : -45.8401447 Eh change ΔE -0.3413518E-09 Eh
gradient norm : 0.0000206 Eh/α predicted 0.0000000E+00 (-100.00%)
displ. norm : NaN α lambda 0.0000000E+00
maximum displ.: NaN α in ANC's SAS scaling and pKa calculations #1, SAS scaling and pKa calculations #1, SAS scaling and pKa calculations #1, ...
converged δE/grad : True / True
*** GEOMETRY OPTIMIZATION CONVERGED AFTER 1 ITERATIONS ***
total energy gain : -0.0000000 Eh -0.0000 kcal/mol
total RMSD : -1.0000000 a0 -0.5292 Å
SUCCESS!
geometry successfully optimized!
FINAL CALCULATION SUMMARY
Output structure:
30
O NaN NaN NaN
C NaN NaN NaN
H NaN NaN NaN
C NaN NaN NaN
C NaN NaN NaN
C NaN NaN NaN
H NaN NaN NaN
O NaN NaN NaN
C NaN NaN NaN
C NaN NaN NaN
C NaN NaN NaN
H NaN NaN NaN
C NaN NaN NaN
O NaN NaN NaN
C NaN NaN NaN
C NaN NaN NaN
O NaN NaN NaN
H NaN NaN NaN
H NaN NaN NaN
H NaN NaN NaN
H NaN NaN NaN
H NaN NaN NaN
H NaN NaN NaN
H NaN NaN NaN
H NaN NaN NaN
H NaN NaN NaN
H NaN NaN NaN
H NaN NaN NaN
H NaN NaN NaN
H NaN NaN NaN
Optimized geometry written to crestopt.xyz
TOTAL ENERGY -45.8401447081 Eh
GRADIENT NORM 0.0000238999 Eh/a0
Wall Time Summary
CREST runtime (total) 0 d, 0 h, 0 min, 0.327 sec
Geometry optimization ... 0 min, 0.120 sec ( 36.827%)
I/O and setup ... 0 min, 0.207 sec ( 63.173%)
CREST terminated normally.
The NaN issue is puzzling and i have tried several different ways to get a different result. I'm not sure where to proceed from this and would like any feedback on this matter.
(If there's no error with the software, im also guessing if i have to perform constrained conformational sampling instead for this molecule (?)).
Kind regards,
hehe.
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