| 10:40:26 PM PDT - Mon, Sep 2nd 2013 |
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I finally tried to define two different MM carbon atoms in my PSPW QM/MM, aka the two different carbons of ethanol, which is my solvent. They have different partial charges and Lennard Jones parameters, hence they need different MM pseudopotentials created, different entries into libraryps/pspw_default/, and the LJ parameters need to be defined for their atom type in the input file.
Let me give you some background - initially I just had one type of MM carbon atom, so I created the C^ file in libraryps/pspw_default/. At the time all of the carbons in my MM section were just listed C (but then they are made into C^ when the mm tags are applied by my mm_tags command), and a C^ psp was created with the mm_psp C^ command after which it was compiled into C^.vpp. C^ LJ parameters were also defined in the input file and interactions between C^ and the rest of the atom types in the simulation were printed in the output file.
When trying to switch to two different types of MM C atoms, I labeled all of the Cs in my MM section C1 and C2, respectively. I created entries C1^ and C2^ in the library, called mm_psp C1^ and mm_psp C2^, and defined their LJ parameters in the input file. I also deleted C^ psps and vpps from my directory, as well as deleting the C^ entry in the library, since I figured they were not necessary. However, this failed to run because it could not find the C^ library entry - despite the fact that I didn't have a C^ type atom in my entire MM section nor any other reference to such an atom type throughout my input.
So then I put a C^ entry back into the library, setting its parameters to those of C1. The program then successfully ran, but while it did make C1^ and C2^ psps, as it was forced to with mm_psp C1^ and mm_psp C2^, it didn't compile them into vpps. Additionally, it did not use the C1^ or C2^ LJ parameters and did not list interactions between C1^ and C2^ mm atoms and the rest of the atoms in the system. However, it did report C^ LJ parameters (which were automatically set to a default of 0.0 and 0.0 because I did not list them in the input file), and it did list C^ interactions with the rest of the atoms.
End result is it clearly is not using C1^ and C2^ and I've no idea how to make it do so. Any help would be greatly appreciated!
Sam
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