Hello everyone,
I'm trying to optimize a qmmm system.
Actually, what I really want to do is to calculate the Free energy of the system.
I saw the documentation page and found that I need .top / .rst / .xyzi / .esp files.
I think I can make .top and .rst file from prepare task, and .xyzi file by manual change of .xyz file.
I also found that .esp file can be obtained by optimization task or esp task.
At first I tried to do esp task but found a error. (I also want to ask about this error later...)
So now I'm trying to do optimize task.
When I run the NWCHEM, the calculation starts and the output file shows no error message.
The problem is that the calculation does not end.
When I open the output file (I'm using openmpi and able to open the .out file during calculation),
I see that the output file remains at certain script line and do not proceed anymore.
Now I'm waiting more than one hour.
I'm not sure whether NWCHEM need more time to proceed or not.
However the energy calculation in my task finished within 100sec. So I guess there is some error.
Here is the description about my system, the input file, and the last output script line
[System] I set solvation box and there is a amino-acid(tyrosine?) at the center.
[Input file]
start tyr
permanent_dir ./perm
scratch_dir ./scratch
md
system tyr_optimization
end
basis
* library "6-31G"
end
dft
xc b3lyp
iterations 500
convergence energy 1e-4
end
qmmm
region qm solvent
maxiter 100 1000
ncycles 5
density espfit
xyz xyz_tyr
end
task qmmm dft optimize
[Tail part of .out file]
NWChem DFT Gradient Module
--------------------------
charge = 0.00
wavefunction = closed shell
DFT ENERGY GRADIENTS
atom coordinates gradient
x y z x y z
1 C 1.020943 0.501344 -16.556675 0.027611 0.049265 0.023862
2 C 1.773129 -1.571252 -18.366403 0.025040 0.042327 -0.018517
3 C 0.631624 1.664066 -12.032204 -0.069200 0.003572 -0.033601
4 C -1.865233 1.828028 -11.172846 -0.008663 0.012754 0.010223
5 C -2.562252 3.750972 -9.495472 0.002641 -0.006136 -0.001670
6 C -0.764556 5.511519 -8.677121 -0.007786 0.014917 0.011669
7 C 1.732301 5.347557 -9.536479 0.002912 0.006850 0.009406
8 C 2.429895 3.423401 -11.215184 -0.000962 -0.008045 -0.005092
9 O -1.447872 7.392487 -7.036097 0.016169 -0.010029 -0.005915
10 N -1.693860 1.171657 -16.968381 0.012055 -0.009052 0.010000
11 C 0.000000 0.000000 22.490492 -0.005057 -0.003997 0.000969
12 O 3.471800 -1.216304 -19.884409 -0.068289 -0.054912 0.043898
13 O 0.639003 -3.686918 -18.306816 0.059139 0.027121 -0.019370
14 H -3.252258 0.469040 -11.803776 0.005123 0.006214 -0.003917
15 H -4.488996 3.877038 -8.832874 0.000656 -0.000740 -0.000128
16 H 3.119014 6.703927 -8.905982 -0.006194 -0.005727 -0.002011
17 H 4.356638 3.297336 -11.877782 -0.001450 -0.000934 -0.002433
18 H 0.213826 -2.067097 -13.511057 0.002625 -0.021090 0.047741
19 H 3.360676 -0.896246 -13.542224 0.022445 -0.034114 -0.045208
20 H 0.000000 8.447355 -6.654673 -0.003146 -0.001115 -0.006300
21 H 2.192494 2.159561 -16.886554 0.000203 -0.004876 -0.017041
22 H -1.940646 1.787807 -18.807798 0.006793 -0.005791 -0.001579
23 H -2.209890 2.593044 -15.727386 0.001415 0.004297 0.002539
24 H -2.808210 -0.405021 -16.653135 -0.011433 -0.002005 0.003300
----------------------------------------
| Time | 1-e(secs) | 2-e(secs) |
----------------------------------------
| CPU | 0.12 | 1.12 |
----------------------------------------
| WALL | 0.12 | 1.12 |
----------------------------------------
Bq nuclear interaction energy = 0.862503323818484
From the last line, calculation does not proceed anymore...
I see that even now, I mean when the calculation does not proceed anymore at above line, the NWCHEM is using memories and CPUs of computer.
Now I have no idea... Can you help me?
Thank you much in advance-
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