Re: Regarding free energy

From: Brian Radak (brian.radak_at_gmail.com)
Date: Mon Dec 10 2018 - 11:47:27 CST

The essential components of this are covered in the NAMD User's Guide and
the tutorial for "in silico alchemy" - I strongly suggest taking a look.

By choosing completely separate schedules for the scaling of electrostatic
and van der Waals interactions (e.g. alchVdwLambdaEnd = alchElecLambdaStart
= 0.5) you can notionally uncouple the two. Note that:

1) This really only works when you have a single alchemical group.
2) The decoupling is essentially arbitrary, since only the net free energy
difference is independent of the choice of schedule.

HTH,
BKR

On Sun, Dec 9, 2018 at 11:33 PM Abhishek Kumar Singh <bo13m1002_at_iith.ac.in>
wrote:

> Dear NAMD users,
>
> I want to decompose the calculated free energy change into the VDW and
> electrostatic part. Please let me know how I can I do it ?
>
> Best Regards,
> Abhishek
>

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