Re: Excluding non bonded interactions between segments

From: Jérôme Hénin (
Date: Tue Apr 08 2014 - 06:56:22 CDT

Hi Fotis,

----- Original Message -----
> Hello Jerome,
> Thank you for your answer. I managed to do the required changes in my PSF
> using Alchemify, with a slight modification to its source code.
> However, having done that, and after reading the alchemical FEP tutorial,
> I have two questions:
> 1)In the FEP tutorial, it is stated that NAMD versions 2.7b2 and later
> will discard terms automatically, and therefore alchemify is not needed
> (this is also mentioned in the alchemify web page). Does this mean that,
> in order for NAMD to read and use the alchemify non-bonded exclusions I
> have defined in my PSF, I have to use a pre 2.7 version of NAMD? (I have
> been using 2.9 and the latest nightly build in my simulations).

No, recent versions of NAMD will create necessary exclusions in FEP runs, but they will also apply those defined explicitly in the PSF.

> 2)Will NAMD honor these exclusions in a typical minimizations? Or should I
> somehow set up a "dummy" FEP simulation to trick the software into using
> them?

The exclusions apply in general, they don't depend on FEP being active.


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