Re: [gmx-users] g_dipole: dipole moment autocorrelation function
On Wed, 2011-03-30 at 20:23 +0200, David van der Spoel wrote: On 2011-03-30 20.16, Nilesh Dhumal wrote: Thanks. How can I take average. summing up and dividing by the number of sims. How much long I should run the simulation. until the average converges. Nilesh On Wed, March 30, 2011 12:59 pm, David van der Spoel wrote: On 2011-03-30 18.54, Nilesh Dhumal wrote: Hello, I am trying to calculate the dipole moment autocorrelation function for my system (ionic liquid). I am using gromacs 4.0.7 version. Hello, I think you will get into some trouble when you try to calculate an autocorrelation function of property that is not continuous in time. In an ionic liquid you have contributions of the molecular dipole and contribution of the charged molecules to the dipole. The latter part is unfortunately not continuous due to jumping of the molecules over the PBCs. It depends what kind of property you want to calculate, but we experienced that simulations in the range of 50-100ns are required to reliably determine properties like the dielectric constant. The next point is that you have to save your coordinates and velocities quite often ( every 0.02ps we used) Check corresponding literature for further advice. Cheers, Flo I run the simulation for 4 ns. I run the following command to calculate the dipole moment autocorrelation function g_dipoles -f water.trr -s water.tpr -corr total -c The function is not geting converge to zero. I want to use this data for calculation of power spectra by fourier transfom of dipole moment autocorrelation function. Can you tell why its not geting converge to zero? You have to simulate at least a few 10s of ns for such slow liquids to converge. Alternatively you can average over many independent simulations (10s). Thanks Nilesh -- 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/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 -- 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 -- Florian Dommert Dipl. - Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart EMail: domm...@icp.uni-stuttgart.de Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert Tel.: +49 - (0)711 - 68563613 Fax.: +49 - (0)711 - 68563658 signature.asc Description: This is a digitally signed message part -- 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: [gmx-users] g_dipole: dipole moment autocorrelation function
On 2011-03-31 09.25, Dommert Florian wrote: On Wed, 2011-03-30 at 20:23 +0200, David van der Spoel wrote: On 2011-03-30 20.16, Nilesh Dhumal wrote: Thanks. How can I take average. summing up and dividing by the number of sims. How much long I should run the simulation. until the average converges. Nilesh On Wed, March 30, 2011 12:59 pm, David van der Spoel wrote: On 2011-03-30 18.54, Nilesh Dhumal wrote: Hello, I am trying to calculate the dipole moment autocorrelation function for my system (ionic liquid). I am using gromacs 4.0.7 version. Hello, I think you will get into some trouble when you try to calculate an autocorrelation function of property that is not continuous in time. In an ionic liquid you have contributions of the molecular dipole and contribution of the charged molecules to the dipole. The latter part is unfortunately not continuous due to jumping of the molecules over the PBCs. It depends what kind of property you want to calculate, but we experienced that simulations in the range of 50-100ns are required to reliably determine properties like the dielectric constant. The next point is that you have to save your coordinates and velocities quite often ( every 0.02ps we used) Check corresponding literature for further advice. Thanks Florian, for pointing that out. I forgot about it in my previous mail. In order to compute the dielectric constant one could in principle apply constant electric fields at different strengths and then extrapolate to zero. Don't know whether that has been done. Cheers, Flo I run the simulation for 4 ns. I run the following command to calculate the dipole moment autocorrelation function g_dipoles -f water.trr -s water.tpr -corr total -c The function is not geting converge to zero. I want to use this data for calculation of power spectra by fourier transfom of dipole moment autocorrelation function. Can you tell why its not geting converge to zero? You have to simulate at least a few 10s of ns for such slow liquids to converge. Alternatively you can average over many independent simulations (10s). Thanks Nilesh -- 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/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 -- 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 -- 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/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: [gmx-users] g_dipole: dipole moment autocorrelation function
On Thu, 2011-03-31 at 10:39 +0200, David van der Spoel wrote: On 2011-03-31 09.25, Dommert Florian wrote: On Wed, 2011-03-30 at 20:23 +0200, David van der Spoel wrote: On 2011-03-30 20.16, Nilesh Dhumal wrote: Thanks. How can I take average. summing up and dividing by the number of sims. How much long I should run the simulation. until the average converges. Nilesh On Wed, March 30, 2011 12:59 pm, David van der Spoel wrote: On 2011-03-30 18.54, Nilesh Dhumal wrote: Hello, I am trying to calculate the dipole moment autocorrelation function for my system (ionic liquid). I am using gromacs 4.0.7 version. Hello, I think you will get into some trouble when you try to calculate an autocorrelation function of property that is not continuous in time. In an ionic liquid you have contributions of the molecular dipole and contribution of the charged molecules to the dipole. The latter part is unfortunately not continuous due to jumping of the molecules over the PBCs. It depends what kind of property you want to calculate, but we experienced that simulations in the range of 50-100ns are required to reliably determine properties like the dielectric constant. The next point is that you have to save your coordinates and velocities quite often ( every 0.02ps we used) Check corresponding literature for further advice. Thanks Florian, for pointing that out. I forgot about it in my previous mail. In order to compute the dielectric constant one could in principle apply constant electric fields at different strengths and then extrapolate to zero. Don't know whether that has been done. In the ionic liquids commmunity dielectric spectra of ILs are usually calulated from equilibrium MD without application of an E-field. The generalized dielectric constant is calculated and a Fourier Laplace transformation finally allows to determine the full dielectric spectrum. Schröder et. al from the University of Vienna have published some articles about this topic. Cheers, Flo Cheers, Flo I run the simulation for 4 ns. I run the following command to calculate the dipole moment autocorrelation function g_dipoles -f water.trr -s water.tpr -corr total -c The function is not geting converge to zero. I want to use this data for calculation of power spectra by fourier transfom of dipole moment autocorrelation function. Can you tell why its not geting converge to zero? You have to simulate at least a few 10s of ns for such slow liquids to converge. Alternatively you can average over many independent simulations (10s). Thanks Nilesh -- 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/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 -- 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 -- 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 -- Florian Dommert Dipl. - Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart EMail: domm...@icp.uni-stuttgart.de Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert Tel.: +49 - (0)711 - 68563613 Fax.: +49 - (0)711 - 68563658 signature.asc Description: This is a digitally signed message part -- 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: [gmx-users] g_dipole: dipole moment autocorrelation function
Thanks Flo for detail reply. Is it possible to put PBC off during calculation of dipole moment autocorrelation function. I will run the simulation for 50ns ans try to save trajectroy of 0.02ps. Thanks NIlesh Nilesh On Thu, March 31, 2011 5:38 am, Dommert Florian wrote: On Thu, 2011-03-31 at 10:39 +0200, David van der Spoel wrote: On 2011-03-31 09.25, Dommert Florian wrote: On Wed, 2011-03-30 at 20:23 +0200, David van der Spoel wrote: On 2011-03-30 20.16, Nilesh Dhumal wrote: Thanks. How can I take average. summing up and dividing by the number of sims. How much long I should run the simulation. until the average converges. Nilesh On Wed, March 30, 2011 12:59 pm, David van der Spoel wrote: On 2011-03-30 18.54, Nilesh Dhumal wrote: Hello, I am trying to calculate the dipole moment autocorrelation function for my system (ionic liquid). I am using gromacs 4.0.7 version. Hello, I think you will get into some trouble when you try to calculate an autocorrelation function of property that is not continuous in time. In an ionic liquid you have contributions of the molecular dipole and contribution of the charged molecules to the dipole. The latter part is unfortunately not continuous due to jumping of the molecules over the PBCs. It depends what kind of property you want to calculate, but we experienced that simulations in the range of 50-100ns are required to reliably determine properties like the dielectric constant. The next point is that you have to save your coordinates and velocities quite often ( every 0.02ps we used) Check corresponding literature for further advice. Thanks Florian, for pointing that out. I forgot about it in my previous mail. In order to compute the dielectric constant one could in principle apply constant electric fields at different strengths and then extrapolate to zero. Don't know whether that has been done. In the ionic liquids commmunity dielectric spectra of ILs are usually calulated from equilibrium MD without application of an E-field. The generalized dielectric constant is calculated and a Fourier Laplace transformation finally allows to determine the full dielectric spectrum. Schröder et. al from the University of Vienna have published some articles about this topic. Cheers, Flo Cheers, Flo I run the simulation for 4 ns. I run the following command to calculate the dipole moment autocorrelation function g_dipoles -f water.trr -s water.tpr -corr total -c The function is not geting converge to zero. I want to use this data for calculation of power spectra by fourier transfom of dipole moment autocorrelation function. Can you tell why its not geting converge to zero? You have to simulate at least a few 10s of ns for such slow liquids to converge. Alternatively you can average over many independent simulations (10s). Thanks Nilesh -- 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/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 -- 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 -- 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 -- Florian Dommert Dipl. - Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart EMail: domm...@icp.uni-stuttgart.de Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert Tel.: +49 - (0)711 - 68563613 Fax.: +49 - (0)711 - 68563658 -- 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?
Re: [gmx-users] g_dipole: dipole moment autocorrelation function
On Thu, 2011-03-31 at 08:53 -0400, Nilesh Dhumal wrote: Thanks Flo for detail reply. Is it possible to put PBC off during calculation of dipole moment autocorrelation function. No, thats the problem, because the volume of the system will increase and dipole density will decrease, this not what you want. However I've written the tool g_current, that allows to calculate the dielectric constant and terms of which it is composed. Read our paper (DOI: 10.1063/1.3030948), which describes the procedure and look at the help, what the programm can do. Cheers, Flo I will run the simulation for 50ns ans try to save trajectroy of 0.02ps. Thanks NIlesh Nilesh On Thu, March 31, 2011 5:38 am, Dommert Florian wrote: On Thu, 2011-03-31 at 10:39 +0200, David van der Spoel wrote: On 2011-03-31 09.25, Dommert Florian wrote: On Wed, 2011-03-30 at 20:23 +0200, David van der Spoel wrote: On 2011-03-30 20.16, Nilesh Dhumal wrote: Thanks. How can I take average. summing up and dividing by the number of sims. How much long I should run the simulation. until the average converges. Nilesh On Wed, March 30, 2011 12:59 pm, David van der Spoel wrote: On 2011-03-30 18.54, Nilesh Dhumal wrote: Hello, I am trying to calculate the dipole moment autocorrelation function for my system (ionic liquid). I am using gromacs 4.0.7 version. Hello, I think you will get into some trouble when you try to calculate an autocorrelation function of property that is not continuous in time. In an ionic liquid you have contributions of the molecular dipole and contribution of the charged molecules to the dipole. The latter part is unfortunately not continuous due to jumping of the molecules over the PBCs. It depends what kind of property you want to calculate, but we experienced that simulations in the range of 50-100ns are required to reliably determine properties like the dielectric constant. The next point is that you have to save your coordinates and velocities quite often ( every 0.02ps we used) Check corresponding literature for further advice. Thanks Florian, for pointing that out. I forgot about it in my previous mail. In order to compute the dielectric constant one could in principle apply constant electric fields at different strengths and then extrapolate to zero. Don't know whether that has been done. In the ionic liquids commmunity dielectric spectra of ILs are usually calulated from equilibrium MD without application of an E-field. The generalized dielectric constant is calculated and a Fourier Laplace transformation finally allows to determine the full dielectric spectrum. Schröder et. al from the University of Vienna have published some articles about this topic. Cheers, Flo Cheers, Flo I run the simulation for 4 ns. I run the following command to calculate the dipole moment autocorrelation function g_dipoles -f water.trr -s water.tpr -corr total -c The function is not geting converge to zero. I want to use this data for calculation of power spectra by fourier transfom of dipole moment autocorrelation function. Can you tell why its not geting converge to zero? You have to simulate at least a few 10s of ns for such slow liquids to converge. Alternatively you can average over many independent simulations (10s). Thanks Nilesh -- 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/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 -- 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 -- 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 -- Florian Dommert Dipl. - Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart EMail: domm...@icp.uni-stuttgart.de Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert Tel.: +49 - (0)711 - 68563613 Fax.: +49 - (0)711 - 68563658 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users
[gmx-users] g_dipole: dipole moment autocorrelation function
Hello, I am trying to calculate the dipole moment autocorrelation function for my system (ionic liquid). I am using gromacs 4.0.7 version. I run the simulation for 4 ns. I run the following command to calculate the dipole moment autocorrelation function g_dipoles -f water.trr -s water.tpr -corr total -c The function is not geting converge to zero. I want to use this data for calculation of power spectra by fourier transfom of dipole moment autocorrelation function. Can you tell why its not geting converge to zero? Thanks Nilesh -- 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: [gmx-users] g_dipole: dipole moment autocorrelation function
On 2011-03-30 18.54, Nilesh Dhumal wrote: Hello, I am trying to calculate the dipole moment autocorrelation function for my system (ionic liquid). I am using gromacs 4.0.7 version. I run the simulation for 4 ns. I run the following command to calculate the dipole moment autocorrelation function g_dipoles -f water.trr -s water.tpr -corr total -c The function is not geting converge to zero. I want to use this data for calculation of power spectra by fourier transfom of dipole moment autocorrelation function. Can you tell why its not geting converge to zero? You have to simulate at least a few 10s of ns for such slow liquids to converge. Alternatively you can average over many independent simulations (10s). Thanks Nilesh -- 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/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: [gmx-users] g_dipole: dipole moment autocorrelation function
Thanks. How can I take average. How much long I should run the simulation. Nilesh On Wed, March 30, 2011 12:59 pm, David van der Spoel wrote: On 2011-03-30 18.54, Nilesh Dhumal wrote: Hello, I am trying to calculate the dipole moment autocorrelation function for my system (ionic liquid). I am using gromacs 4.0.7 version. I run the simulation for 4 ns. I run the following command to calculate the dipole moment autocorrelation function g_dipoles -f water.trr -s water.tpr -corr total -c The function is not geting converge to zero. I want to use this data for calculation of power spectra by fourier transfom of dipole moment autocorrelation function. Can you tell why its not geting converge to zero? You have to simulate at least a few 10s of ns for such slow liquids to converge. Alternatively you can average over many independent simulations (10s). Thanks Nilesh -- 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/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: [gmx-users] g_dipole: dipole moment autocorrelation function
On 2011-03-30 20.16, Nilesh Dhumal wrote: Thanks. How can I take average. summing up and dividing by the number of sims. How much long I should run the simulation. until the average converges. Nilesh On Wed, March 30, 2011 12:59 pm, David van der Spoel wrote: On 2011-03-30 18.54, Nilesh Dhumal wrote: Hello, I am trying to calculate the dipole moment autocorrelation function for my system (ionic liquid). I am using gromacs 4.0.7 version. I run the simulation for 4 ns. I run the following command to calculate the dipole moment autocorrelation function g_dipoles -f water.trr -s water.tpr -corr total -c The function is not geting converge to zero. I want to use this data for calculation of power spectra by fourier transfom of dipole moment autocorrelation function. Can you tell why its not geting converge to zero? You have to simulate at least a few 10s of ns for such slow liquids to converge. Alternatively you can average over many independent simulations (10s). Thanks Nilesh -- 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/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 -- 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/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] g_dipole: dipole moment autocorrelation function: Bug?
Hello, I am trying to calculate the non normalized dipole moment autocorrelation function for water. I am using flexible spc water model (define=-DFLEX_SPC). I am using gromacs 4.0.7 version. I run the simulation for 4 ns. I run the following command to calculate the dipole moment autocorrelation function g_dipoles -f water.trr -s water.tpr -nonormalize -corr total -c I am geting the really high values around +5000 and -100 (dipcorr.xvg). Is there anything wrong and function is not geting converge to zero? I didn't get reply. Does it a bug? Where should I file the bug. Thanks Nilesh -- 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] g_dipole: dipole moment autocorrelation function: Bug?
Hello, I am trying to calculate the non normalized dipole moment autocorrelation function for water. I am using flexible spc water model (define=-DFLEX_SPC). I am using gromacs 4.0.7 version. I run the simulation for 4 ns. I run the following command to calculate the dipole moment autocorrelation function g_dipoles -f water.trr -s water.tpr -nonormalize -corr total -c I am geting the really high values around +5000 and -100 (dipcorr.xvg). Is there anything wrong and function is not geting converge to zero? I didn't get reply. Does it a bug? Where should I file the bug. Thanks Nilesh -- 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] g_dipole: dipole moment autocorrelation function
Hello, I am trying to calculate the non normalized dipole moment autocorrelation function for water. I am using flexible spc water model (define=-DFLEX_SPC). I am using gromacs 4.0.7 version. I run the simulation for 4 ns. I run the following command to calculate the dipole moment autocorrelation function g_dipoles -f water.trr -s water.tpr -nonormalize -corr total -c I am geting the really high values around +5000 and -100 (dipcorr.xvg). Is there anything wrong and function is not geting converge to zero? Thanks Nilesh -- 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
