Re: [gmx-users] correlation function 'time value' ?
Dear Mark and David, Thanks you, i will check the paper very carefully and try again. regards, Rama On Sat, Feb 27, 2010 at 1:13 AM, Mark Abraham mark.abra...@anu.edu.auwrote: On 27/02/2010 7:31 PM, Ramachandran G wrote: Dear Dr. van der Spoel: Thanks for the clarification in your reply. One more thing I was just curious is that, for C(t) = f(x).f(x+t) , what is the default value for t, which is often called correlation time, in gromacs for correlation function calculation, especially in g_hbond, and/or is it possible to customize the t in gromacs? t is not the correlation time. t is an arbitrary amount of time, at which the magnitude of C(t) indicates the extent to which f is correlated with itself when a set of samples are examined at time interval t. The (integrated) correlation time is the integral of (normalized) C(t) over 0 t infinity. See section 8.5 of the manual. I also found the explanations in Wolff, U. Comput. Phys. Commun. 2004, 156, 143-153. Madras, N.; Sokal, A. D. J. Stat. Phys. 1988, 50, 109-186. useful. Mark On Fri, Feb 26, 2010 at 10:03 PM, David van der Spoel sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se wrote: On 2010-02-27 03.27, Ramachandran G wrote: Hi gromacs users: As you know autocorrelation function C(t) C(t) = f(0).f(t) 't' value can start from 0 but, i would like to know what value does gromacs use, more specifically for g_hbond. Can anyone help me? Thank you. Rama The tell you that all time origins x are used, so C(t) = f(x).f(x+t) _x -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se http://folding.bmc.uu.se -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Postdoctoral Research Scholar, Department of Chemistry, University of Nevada, Reno. -- 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 -- Postdoctoral Research Scholar, Department of Chemistry, University of Nevada, Reno. -- 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
Re: [gmx-users] correlation function 'time value' ?
Dear Dr. van der Spoel: Thanks for the clarification in your reply. One more thing I was just curious is that, for C(t) = f(x).f(x+t) , what is the default value for t, which is often called correlation time, in gromacs for correlation function calculation, especially in g_hbond, and/or is it possible to customize the t in gromacs? best Rama On Fri, Feb 26, 2010 at 10:03 PM, David van der Spoel sp...@xray.bmc.uu.sewrote: On 2010-02-27 03.27, Ramachandran G wrote: Hi gromacs users: As you know autocorrelation function C(t) C(t) = f(0).f(t) 't' value can start from 0 but, i would like to know what value does gromacs use, more specifically for g_hbond. Can anyone help me? Thank you. Rama The tell you that all time origins x are used, so C(t) = f(x).f(x+t) _x -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- 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 -- Postdoctoral Research Scholar, Department of Chemistry, University of Nevada, Reno. -- 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
Re: [gmx-users] correlation function 'time value' ?
On 2010-02-27 09.31, Ramachandran G wrote: Dear Dr. van der Spoel: Thanks for the clarification in your reply. One more thing I was just curious is that, for C(t) = f(x).f(x+t) , what is the default value for t, which is often called correlation time, in gromacs for correlation function calculation, especially in g_hbond, and/or is it possible to customize the t in gromacs? The correlation time is a result from the calculation. There are many definitions possible. One is the integral of C(t). JPCB 110 (2006) p. 4393 gives explanations for hbonds. best Rama On Fri, Feb 26, 2010 at 10:03 PM, David van der Spoel sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se wrote: On 2010-02-27 03.27, Ramachandran G wrote: Hi gromacs users: As you know autocorrelation function C(t) C(t) = f(0).f(t) 't' value can start from 0 but, i would like to know what value does gromacs use, more specifically for g_hbond. Can anyone help me? Thank you. Rama The tell you that all time origins x are used, so C(t) = f(x).f(x+t) _x -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se http://folding.bmc.uu.se -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Postdoctoral Research Scholar, Department of Chemistry, University of Nevada, Reno. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- 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
Re: [gmx-users] correlation function 'time value' ?
On 27/02/2010 7:31 PM, Ramachandran G wrote: Dear Dr. van der Spoel: Thanks for the clarification in your reply. One more thing I was just curious is that, for C(t) = f(x).f(x+t) , what is the default value for t, which is often called correlation time, in gromacs for correlation function calculation, especially in g_hbond, and/or is it possible to customize the t in gromacs? t is not the correlation time. t is an arbitrary amount of time, at which the magnitude of C(t) indicates the extent to which f is correlated with itself when a set of samples are examined at time interval t. The (integrated) correlation time is the integral of (normalized) C(t) over 0 t infinity. See section 8.5 of the manual. I also found the explanations in Wolff, U. Comput. Phys. Commun. 2004, 156, 143-153. Madras, N.; Sokal, A. D. J. Stat. Phys. 1988, 50, 109-186. useful. Mark On Fri, Feb 26, 2010 at 10:03 PM, David van der Spoel sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se wrote: On 2010-02-27 03.27, Ramachandran G wrote: Hi gromacs users: As you know autocorrelation function C(t) C(t) = f(0).f(t) 't' value can start from 0 but, i would like to know what value does gromacs use, more specifically for g_hbond. Can anyone help me? Thank you. Rama The tell you that all time origins x are used, so C(t) = f(x).f(x+t) _x -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se http://folding.bmc.uu.se -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Postdoctoral Research Scholar, Department of Chemistry, University of Nevada, Reno. -- 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] correlation function 'time value' ?
Hi gromacs users: As you know autocorrelation function C(t) C(t) = f(0).f(t) 't' value can start from 0 but, i would like to know what value does gromacs use, more specifically for g_hbond. Can anyone help me? Thank you. Rama -- 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
Re: [gmx-users] correlation function 'time value' ?
On 2010-02-27 03.27, Ramachandran G wrote: Hi gromacs users: As you know autocorrelation function C(t) C(t) = f(0).f(t) 't' value can start from 0 but, i would like to know what value does gromacs use, more specifically for g_hbond. Can anyone help me? Thank you. Rama The tell you that all time origins x are used, so C(t) = f(x).f(x+t) _x -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- 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
