<html><head><meta http-equiv=Content-Type content="text/html; charset=iso-8859-1"><META name="Author" content="Novell GroupWise WebAccess"></head><body style='font-family: Tahoma, sans-serif; font-size: 13px; '>Hi,<br><br>You could calculate the number of H-bonds with the option -num .<br>Out of this x,y plot you have the possibility to calculate the correlation time by the H-bond<br>autocorrelation function < Number-of-Hbonds (t), Number-of-Hbonds (t_0) >.<br>This H-bond correlation-time could be equal to the residence time, because<br>it is equal to the average H-bond-existence time.<br>The correlation time is the time until the H-bond-correlation function shows no<br>correlated configuration any more. <br><br>At least from my experience - <br><br>Bests,<br><br>Emanuel<br><br>>>> Mark Abraham <Mark.Abraham@anu.edu.au> 22.08.11 12.01 Uhr >>><br>On 22/08/2011 6:22 PM, aiswarya pawar wrote:<br>> Hi,<br>><br>> I have simulated a protein complex and now i would like to know the <br>> residing water molecules between the protein complex. g_hbond and <br>> trjorder helps in giving the number of hydrogen bonds and distance. <br>> but is this the residence time calculation. please help me with this. <br>> there few posts given in the archives regarding the residence time <br>> which is not very clear to me. but will the residence time calculation <br>> same for single protein and complex<br><br>Please do not cross-post requests for help to the mailing list and <br>private individuals who have not advertised interest in such personal <br>email. I do not even know what the definition of an H-bond residence <br>time is. Hopefully somebody who does is reading the list.<br><br>Mark<br>-- <br>gmx-users mailing list gmx-users@gromacs.org<br>http://lists.gromacs.org/mailman/listinfo/gmx-users<br>Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!<br>Please don't post (un)subscribe requests to the list. Use the <br>www interface or send it to gmx-users-request@gromacs.org.<br>Can't post? Read http://www.gromacs.org/Support/Mailing_Lists<br></body></html>