[gmx-users] Fwd: g_select or g_trjorder

[Apramita Chand]

With reference to my earlier query, I would like to add that when I use
g_select, it gives me an average of 9-10 solute molecules around reference
protein while when I use g_trjorder , I get 20-23 molecules on an average.

Why are the number of molecules different in both cases ? Which should be
considered if I want to use these values for calculation of preferential
interaction coefficient?



---------- Forwarded message ---------
From: Apramita Chand <apramita.chand at gmail.com>
Date: Thu, Jun 7, 2018, 3:42 PM
Subject: g_select or g_trjorder
To: <gmx-users at gromacs.org>


Dear All,
I want to evaluate the preferential interaction coefficient and according
to the equation given in the literature, I want the number of water and
cosolute molecules (nw, nx) for local and bulk regions specified by a
particular cut-off distance from the protein.

There are two options that I have; using g_select or g_trjorder. Which of
the two is more suitable for calculation of the preferential interaction
coefficient?

Yours sincerely,
Apramita