Vasilis Georgilas wrote:
Hello everyone,
in the NPT simulation I run I have 2 layers of water and palmitic acid
in between.
How i should make my index file to see the different kinds of hydrogen
bonds?
ps
there will be water - water , O= ..... O= between PLM, O= ...... OH
between PLM and water and OH .... OH between water and PLM hydrogen bonds
Then you need groups for each of these moieties (water should be a default
group), and you'll have to do several runs of g_hbond to collect all of the
pairs you want to analyze.
-Justin
thanks in advance
Regards,
Vasilis
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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