I think that Qiao is right, and I also think that it's an easy thing to test on
a simple test system consisting of a just a single solute molecule (a single
atom to keep it simple) and just a few solvent molecules (a single one is even
easier).
/Erik Marklund
----- Original Message -----
From: Qiao Baofu
To: Discussion list for GROMACS users
Sent: Wednesday, November 22, 2006 1:39 PM
Subject: Re: [gmx-users] radial distribution function
To my knowledge, g_rdf calculate all the atoms of group A to all the atoms of
group B to get the gAB(r). g_rdf -com calculate the center of group A, not the
centers of the residues in group A to all the atoms of group B.
I upload a file based on gmx_rdf.c to calculate the centers of residues of
group A (and B) last month to the website of gromacs.
2006/11/22, Nguyen Hoang Phuong < [EMAIL PROTECTED]>:
My question is that how does gromacs compute
g(r)? Is r the distance between center of mass
of the group [ Pep ] and the center of mass of each
solvent molecule? Or gromacs computes g_i(r) between
each atom of the group [ Pep] with respect to solvent
molecules and then take average over all g_i(r) to get
g(r)?
Many thanks in advance,
Phuong
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Baofu Qiao
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