Hi, You could calculate the number of H-bonds with the option -num . Out of this x,y plot you have the possibility to calculate the correlation time by the H-bond autocorrelation function < Number-of-Hbonds (t), Number-of-Hbonds (t_0) >. This H-bond correlation-time could be equal to the residence time, because it is equal to the average H-bond-existence time. The correlation time is the time until the H-bond-correlation function shows no correlated configuration any more.
At least from my experience - Bests, Emanuel >>> Mark Abraham 22.08.11 12.01 Uhr >>> On 22/08/2011 6:22 PM, aiswarya pawar wrote: > Hi, > > I have simulated a protein complex and now i would like to know the > residing water molecules between the protein complex. g_hbond and > trjorder helps in giving the number of hydrogen bonds and distance. > but is this the residence time calculation. please help me with this. > there few posts given in the archives regarding the residence time > which is not very clear to me. but will the residence time calculation > same for single protein and complex Please do not cross-post requests for help to the mailing list and private individuals who have not advertised interest in such personal email. I do not even know what the definition of an H-bond residence time is. Hopefully somebody who does is reading the list. Mark -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
-- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
