From NWChem
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| 5:57:57 AM PDT - Tue, Oct 22nd 2013 |
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I am attempting to do a geometry optimization and output the optimized coordinates. I use the "xyz" flag, but the coordinate file is not created. The job runs through succesfully; it just doesn't create a coordinate file as I expect it to. My input file is:
start
md
system test
noshake solute
end
basis
* library 6-311G*
end
dft
xc b3lyp
end
qmmm
region all
density espfit
xyz foo_output_coords
end
task qmmm dft optimize
In the end, there are no files with the tag "foo_output_coords". Do I need an additional command to direct it to write out the coordinate file using that tag?
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Marat Forum:Admin, Forum:Mod, NWChemDeveloper, bureaucrat, sysop
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Posts 43
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| 10:05:42 AM PDT - Tue, Oct 22nd 2013 |
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| It will not print xyz coordinates when you do all region optimization. Given, typically, large size of the system in QM/MM runs the xyz option was only meant for region qm. You can always extract PDB file at the end of the run.
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| 11:06:42 AM PDT - Tue, Oct 22nd 2013 |
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| Thank you for your help! What is the best way to extract the PDB file and which file should I extract it from? I know for output from the Molecular Dynamics module, PDB files can be extracted from the trajectory file (*.trj) using the Analysis module. However, no trajectory file is created from the qmmm dft geometry optimization calculation, and it's unclear to me in which output file the final optimized coordinates can be found. If necessary, I can create a PDB formatted file from raw xyz coordinates, if I just knew how to access the coordinates.
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Posts 19
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| 1:11:55 AM PDT - Wed, Oct 23rd 2013 |
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I don't know if it is the faster way, but to extract the optimized geometry I use a prepare module at the end of the input:
prepare
read file_name_ref.qrs
write file_name_opt.pdb
end
task prepare
Ale
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Edited On 1:13:08 AM PDT - Wed, Oct 23rd 2013 by Varnon
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| 6:06:06 AM PDT - Wed, Oct 23rd 2013 |
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| That's great; thank you for your help!
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