Query: Running simulation with external parameters

[CallumFrEllis]

Hi,

I am trying to run some small simulations usings the parameters listed in the SIs for https://pubs.acs.org/doi/10.1021/jp410720y for a variety of organic solvents.

What is is the best way to use these parameters? Can I create a key file with these, or append them to the Amoeba09.prm or create a new .prm file with only these parameters?

Any help would be appriciated.

Best wishes,

Callum

[jayponder]

Actually, you can do any of the three things you suggest.

Any "extra" parameters needed for the system you are computing can always be added to the key file. In that case you would still use a line in the key file pointing to an AMOEBA parameter file (for example "parameters /Users/ponder/tinker/params/amoeba09.prm" or similar). Parameters found in the key file are read after any main parameter file such as amoeba09.prm. And thus parameters in the key file with the same atom type or class numbers as in the parameter file will be overwritten by the values supplied in the key file.

Alternatively, you could simply add the same extra or new parameters directly into the amoeba09.prm or similar parameter file.

Finally, you could create your own new parameter file. If you choose to do this, then make sure you copy the "header" information for the AMOEBA force field into your new parameter file. This information can be found as the top section of any of the AMOEBA parameter files, and serves to define the energy functions used by the AMOEBA force field.

Hope this helps. Let me know if anything is unclear.

[CallumFrEllis]

Thank you so much for the prompt and very helpful response, I will have a play and see how I get on.

Thanks again,

Callum