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alchemical sterics exclude sigma #682

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Dan-Burns opened this issue Apr 9, 2023 · 2 comments
Open

alchemical sterics exclude sigma #682

Dan-Burns opened this issue Apr 9, 2023 · 2 comments

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@Dan-Burns
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Is the sigma term of the lennard-jones potential affected when alchemically modifying sterics?

If so, I'd like the option to only apply it to epsilon. Can somebody point me to where I can make this edit?
I'm assuming it's in alchemy.py but I can't figure out where.

Thank you,
Dan

@zhang-ivy
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zhang-ivy commented Apr 11, 2023

Is the sigma term of the lennard-jones potential affected when alchemically modifying sterics?

It looks like it is, see: https://github.com/choderalab/openmmtools/blob/main/openmmtools/alchemy.py#L1379-L1380

@Dan-Burns
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Thank you, @zhang-ivy.
I assume I can change the line in exceptions_sterics_energy_expression from:
'reff_sterics = sigma*((softcore_alpha*(1.0-({0}))^softcore_b + (r/sigma)^softcore_c))^(1/softcore_c);')\ .format(lambda_variable_name)
to:
'reff_sterics = sigma*((softcore_alpha*(1.0)^softcore_b + (r/sigma)^softcore_c))^(1/softcore_c);')
I will see what happens.
Dan

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