Re: Excluding non bonded interactions between segments

From: Fotis Baltoumas (
Date: Tue Apr 08 2014 - 06:57:35 CDT

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).
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

Thanks again for your help,

> Hi Fotis,
> NAMD will honor non-bonded exclusions defined in the PSF file, but you
> don't have to edit that file by hand. You can generate the exclusions as
> you would for an alchemical FEP simulation using Alchemify:
> Cheers,
> Jerome

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