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autogenerate command
#36918 03/29/18 08:53 PM
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rossi Offline OP
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Hello:

I want to ask a question about the autogenerate command.

Does

autogen angle dihedral

generate angles and dihedrals ONLY for the atoms which are bonded by a bond command in the RTF.

For example, I am working on a metal cluster with hydrocarbon chains bonded to some of the metal atoms. Some of the metal atoms in the core of the cluster are controlled by only nonbonded forces while metal atoms bonded to other metal atoms have bond terms in the RTF.

Thus the question I have is what angles and dihedral angles be generated by use of the autogenerate command?

I hope that only atoms with the bond term in the RTF will have the corresponding angles and dihedral angles.

Thanks so much for your help with this.

Regards,
Angelo

Re: autogenerate command
rossi #36919 03/29/18 09:10 PM
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Your assumption is correct; the bonded topology is used by AUTOGEN to determine which angles and dihedrals to add to the PSF.


Rick Venable
computational chemist

Re: autogenerate command
rmv #36920 03/30/18 05:28 PM
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rossi Offline OP
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Thank you.

Regards,

Angelo


Moderated by  lennart, rmv 

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