[gmx-users] g_tune_pme in Ranger
Hi, I wonder whether somebody has been able to install g_tune_pme in Ranger (one of the tacc clusters). If so, please contact me off list as I have a couple of questions to ask. Patricia. -- Dr. Patricia Soto patricia.sot...@gmail.com ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Re: HB lifetime in g_hbond
I have a question regarding the calculation of hydrogen bond lifetimes in g_hbond: Line 1094 of gmx_hbond.c v 1.16.2.11 2006/04/02 (which is equivalent to line 1121 of gmx_hbond.c v 1.28 2006/08/30) reads: t = hb-time[i] - hb-time[0] - 0.5*dt; leading to the time series 1, 3, 5,.. that does not correspond to my sampling frequency of 2ps. This affects the calculation of x1 in the immediate next line. My question is: Why is t defined in this way? The program computes an histogram and centers the points in between time points. Note that this flag gives you useless lifetimes, see J. Phys. Chem. B 110 pp. 4393-4398 (2006). You want to use the lifetime that comes from the -ac option (look at line with Forward) Yes, I had indeed noticed that the value reported by this flag was far from my own calculations so I wanted to make sure I was understanding what g_hbond was doing. Thanks. (of course, I already read your paper in JPC B.) Patricia ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] HB lifetime in g_hbond
Hi, I have a question regarding the calculation of hydrogen bond lifetimes in g_hbond: Line 1094 of gmx_hbond.c v 1.16.2.11 2006/04/02 (which is equivalent to line 1121 of gmx_hbond.c v 1.28 2006/08/30) reads: t = hb-time[i] - hb-time[0] - 0.5*dt; leading to the time series 1, 3, 5,.. that does not correspond to my sampling frequency of 2ps. This affects the calculation of x1 in the immediate next line. My question is: Why is t defined in this way? This question was posted in the past but did not find answer in the users list. Thanks! Patricia ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
