Re:

From: Brian Radak (brian.radak_at_gmail.com)
Date: Sun Sep 15 2019 - 18:00:36 CDT

I would recommend reading the tutorial
<http://www.ks.uiuc.edu/Training/Tutorials/namd/tutorial-constant-ph/tutorial-constant-ph.pdf>
or else consulting the relevant portion of the user guide. The cphlog
format is extensively documented. A semi-official but not entirely
supported tool called "cphanalyze" is available with the pynamd pacakge on my
personal GitHub page <https://github.com/radakb/pynamd>. Installation and
usage is covered in the tutorial.

Cheers,
BKR

On Sun, Sep 15, 2019 at 3:37 PM SHOBHIT JAIN . <
f20150817_at_hyderabad.bits-pilani.ac.in> wrote:

> Respected Sir/maam
> I was running a constant pH simulation using namd i wamt to know how to
> calculate the fraction of protonted over deprotonted.
>
> Regards
> Shobhit jain
> Student
> BITS Pilani Hyderabad Campus
>

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