Re: Thermodynamic integration output analysis

From: Brian Radak (brian.radak_at_gmail.com)
Date: Wed Mar 07 2018 - 07:59:18 CST

Unfortunately, I really doubt that anyone is actively maintaining
namd2_ti.pl (I've never even seen an extant copy of the source that I can
recall).

As in previous discussions of TI on this list, I strongly recommend
examining the integrand for your specific case before trying any kind of
automated solution. There are a number of potentially significant sources
of error that can go completely unnoticed if you are not careful.

BKR

On Wed, Mar 7, 2018 at 6:57 AM, Giorgio Amendola <
GIORGIO.AMENDOLA_at_unicampania.it> wrote:

> Dear NAMD users,
>
>
> I'm interested in running relative binding free energy calculations for
> protein/ligand systems using thermodynamic integration.
> However, the available perl script for the TI analysis, namd2_ti.pl,
> doesn't work with the revised output from NAMD 2.12. So, I thought about
> using the 2.11 version of the software, but I'm still having problem when I
> run the script with the outputs from the calculation. I get errors like
> this one "Modification of non-creatable array value attempted, subscript
> -1999 at ./namd2_ti.pl line 102, <FILE> line 210477". I've tried to look
> into the error, and apparently it's about correctly handling the
> equilibration data. Other people have experienced it too, but I couldn't
> find a solution unfortunately.
> I was wondering if any of you could give me some tips on what tools I
> could use to analyze the output of the 2.12 version, or maybe some version
> of namd2_ti.pl that doesn't present this issue.
>
> Thanks
>
>
> Giorgio Amendola
>
>

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