Hi Rasmus, >From your previous email I understood that you have only two molecules (you didn't write that you're using 500 and nothing on the rest of the system). Apparently, this is not the case. I don't think you can get what you want from g_hbond without modifying the source code. If you don't mind 500 runs you can use g_dist -dist, where group 1 is a single hydrogen bond donor oxygen and group two all potential acceptors, find the molecules which satisfy your criterion and then run g_hbond on them if you want to be sure that you have a hydrogen bond that satisfy angle criteria as well. Tedious, but can work with some scripting and patience.
Ran. Rasmus "Termo" Lundsgaard wrote: > Hi Ran. > > If I understand you right, then you suggest to have one molecule as > acceptor, and the rest (499) as donors, and then look in the hbnum.xvg > to see how often there is two hydrogen bonds... > > 1. is that I have to do this check for every molecule. > > 2. there is no guaranty that the two hydrogen bonds are to the same > other molecule - it could very well be as a part of a chain... > > 3. If possible I would like to do measurement of distance between > molecules when they are bonded as a dimer... > > Best regards > Rasmus > > > Ran Friedman wrote: >> Hi Rasmus, >> >> A simple solution would be to run g_hbond twice, with two separate >> groups for acetate 1 as donor and acetate 2 as acceptor or vice versa, >> check the existence an hydrogen bond with g_hbond -num and write a >> script to check when the two hydrogen bonds co-exist. >> >> Hope that helps, >> Ran. >> >> Rasmus "Termo" Lundsgaard wrote: >> >>> Hi All. >>> >>> I'm trying to calculate the Hydrogen bond occupancy when there is two >>> hydrogen bonds between same two acetic acid molecules at the same time. >>> >>> With g_hbond I can get the hbond.ndx giving me "all ocuring hydrogen >>> bonds" group and the hbmap.xpm gives me the matrix of when these >>> hydrogen bonds exist for each timeframe... >>> >>> How can I calculate the occupancy of when two hydrogen bonds exist >>> between the same two molecules?? >>> >>> >>> Best regards >>> Rasmus >>> >> >> >> > -- ------------------------------------------------------ Ran Friedman Postdoctoral Fellow Computational Structural Biology Group (A. Caflisch) Department of Biochemistry University of Zurich Winterthurerstrasse 190 CH-8057 Zurich, Switzerland Tel. +41-44-6355559 Email: r.fried...@bioc.unizh.ch Skype: ran.friedman ------------------------------------------------------
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