On 1/11/13 1:10 PM, Miguel Ángel Mompeán García wrote:
The donors are two H atoms from the amide group of Gln residues. Thus,
I will try the -merge option. Thank for the comment.
I wonder if the following issue is affecting gromacs 4.5.5:
http://lists.gromacs.org/pipermail/gmx-users/2011-May/061249.html
No, that issue was fixed before the 4.5.5 release.
-Justin
2013/1/11, Justin Lemkul <[email protected]>:
On 1/11/13 6:23 AM, Miguel Ángel Mompeán García wrote:
Hi all,
When calculating the average number of hbonds during a simulation, does
the
program g_hbond contemplate the possibility of an atom involved in two
hbond?
If I visualize the structures with molden, setting the same cutoff
criterion for hbonding than g_hbond utilizes, I found out that some O
atoms
are forming two H bonds with two different hydrogen atoms at once. Other
O
atoms are forming just one H bond.
With g_hbond I get the same average on systems when the same O atoms are
forming two hbonds and in those where they form just one.
If the criterion is just a cutoff distance and angle, I guess I should
have
seen the differences when using g_hbond with -num, but this never
happened... Any clue?
For O atoms with two putative H-bonds, are the donors on separate functional
groups or molecules? If they are not, g_hbond considers them the same,
since
that is the default behavior of the -merge option. If you specify -nomerge,
then the two hydrogen bonds will be considered distinct.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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