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