[gmx-users] g_hbond index
jalemkul at vt.edu
Wed Dec 19 18:22:53 CET 2012
On 12/19/12 11:43 AM, Kavyashree M wrote:
> I thought that the order should not matter but when I used 18 - 1
> and 1 - 18 the graph were slightly off.
> Group 18 is a set of residues in that protein with some unique property.
> I wanted to see the variation of Hbond of these residues with the whole
> protein. so group 18 is a subset of group 1.
You see a difference likely because you are invoking the command incorrectly
(with overlapping index groups) and it is affecting the way the donor and
acceptor arrays are constructed. The proper method of analysis is to monitor
H-bonds within "group 18" and then between "group 18" and whatever part of the
protein that does not overlap with it.
Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
More information about the gromacs.org_gmx-users