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] Problem on i7
Hi, I'm facing a problem where the GROMACS can't distribute the job that I send between the 8 nodes of my computer (i7 920). Actually, when I send the job with the command line mpirun -np 8 mdrun (...) each CPU receive the information and perform the job by itself, without distribution. Someone that face this problem (or that know hou to fix it) could help me? Thanks !! -- 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] Problem on i7
Hi, this happens if the mdrun hasn't been compiled with configure --enable-mpi. Roland On Sat, Feb 27, 2010 at 1:04 PM, Maurício Menegatti Rigo mauriciomr1...@gmail.com wrote: Hi, I'm facing a problem where the GROMACS can't distribute the job that I send between the 8 nodes of my computer (i7 920). Actually, when I send the job with the command line mpirun -np 8 mdrun (...) each CPU receive the information and perform the job by itself, without distribution. Someone that face this problem (or that know hou to fix it) could help me? Thanks !! -- 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 -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309 -- 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] Problem on i7
Hi Roland, thanks for your answer. Actually, I installed the GROMACS from Synaptic package manager. I dont know if the manager compile with the --enable-mpi option. I'll try to reinstall with this option and see what happens. Thank you very much!! -- 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] Problem on i7
Hi, Ubuntu has also gromacs-mpich and gromacs-openmpi which contain mdrun_mpi to run in parallel. Roland On Sat, Feb 27, 2010 at 1:53 PM, Maurício Menegatti Rigo mauriciomr1...@gmail.com wrote: Hi Roland, thanks for your answer. Actually, I installed the GROMACS from Synaptic package manager. I dont know if the manager compile with the --enable-mpi option. I'll try to reinstall with this option and see what happens. Thank you very much!! -- 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 -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309 -- 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
