[gmx-users] g_hbond index
hmkvsri at gmail.com
Thu Dec 20 05:24:19 CET 2012
Ok thank you.
On Wed, Dec 19, 2012 at 10:52 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> 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.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
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