alchemlyb: NAMD parser does not take temperature as argument

The NAMD parser #7 (for FEP) does not take T as an argument and does not return u_nk in proper units of kT.

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  • Original URL
  • State: closed
  • Created 5 years ago
  • Comments: 19 (9 by maintainers)

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The BAR and MBAR operate on dimensionless quantities: kT must be in the same units as the energies. Otherwise beta*U becomes something different. . . If BOTH the energies and kT change units, then everything is valid, except of course the free energies will be in those different units.

Currently the software modules assume you are passing in the beta*U quantities (already nondimensionalized). So you multiply the results by whatever kT you divided the energies by before you passed them into BAR.

Thanks for confirming.

Currently, the temperature from the output file is not used, is it?

I don’t think that it would be correct to use the instantaneous temperature for kT – the Boltzmann factor comes from a Lagrange multiplier for system at constant T (i.e., constant average temperature) so this T should be the “target temperature” of the thermostat in the simulation. But maybe @mrshirts @davidlmobley want to correct me here.