Re: Antw: Re: [gmx-users] calculate residence time for a protein complex
Mark, Sorry for the trouble. Aiswarya Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it! -Original Message- From: Emanuel Peter emanuel.pe...@chemie.uni-regensburg.de Sender: gmx-users-boun...@gromacs.org Date: Mon, 22 Aug 2011 12:36:02 To: gmx-users@gromacs.org Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org Subject: Antw: Re: [gmx-users] calculate residence time for a protein complex -- gmx-users mailing listgmx-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 listgmx-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
Re: Antw: Re: [gmx-users] calculate residence time for a protein complex
Dear Emanuel, Thank you so much for the response. I did the H bond count using the g_hbond. After this these H bond are correlated against time right?? I just want to make sure I got it right. And more over I should give a distance constrain so as to give me the existence of water at a time. I just want to be more clear on the correlation function of H bonding. Thank you, Aiswarya Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it! -Original Message- From: Emanuel Peter emanuel.pe...@chemie.uni-regensburg.de Sender: gmx-users-boun...@gromacs.org Date: Mon, 22 Aug 2011 12:36:02 To: gmx-users@gromacs.org Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org Subject: Antw: Re: [gmx-users] calculate residence time for a protein complex -- gmx-users mailing listgmx-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 listgmx-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
Antw: Re: [gmx-users] calculate residence time for a protein complex
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 listgmx-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 listgmx-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
