Re: [gmx-users] Dipole moment
When calculated during the md run, the corresponding options in g_energy for the dipole moment are MU-X, MU-Y and MU-Z. However, taking into account the previous mail by David van der Spoel, it's possible that the dipole moment could not be calculated in your system. Options in g_energy vary depending on the actual computation. If you want to calculate the dipole moment by your own, I think it's easier to use the xtc file exported every 3fs (it'll be considerably heavier than the edr file, however) and writing an specific code for your purposes. In order to read the trajectories, you can use the xtc library (http://www.gromacs.org/Developer_Zone/Programming_Guide/XTC_Library). Anyway, if the code didn't compute it, there should be a reason. Javier El 19/10/12 04:42, Nilesh Dhumal escribió: Is it possible to calcualte the dipole moment at 3fs by modifing the source code? Nilesh How can I save the total dipole moment extacted by .edr file? I could not find the option in g_energy. Nilesh Justin is right. I've slipped a bit, that was not the way to set nstenergy. But still, you can save the dipole directly in the edr file. Not from your existing trajectory, but in a new run. Say your dt=1fs, then you should set nstenergy=3 to get your dipole moment every 3fs which you can retrieve with g_energy. Javier El 18/10/12 20:43, Nilesh Dhumal escribió: In short, I can not save dipole moment directly. I can calculate dipole moment only using .trr file. Nilesh On 10/18/12 1:45 PM, Javier Cerezo wrote: Hi The dipole is stored in the edr file, which output frequency is controlled by nstenergy option in the mdp parameter file. Set it appropriately during your run (nstenergy=0.003) but keep in mind that it should be a multiple of the time step. nstenergy cannot be set this way; it is an integer indicating the interval (in number of steps) for writing energy values. If the values have been saved every 2 ps, there is no way to retrieve them every 3 fs; if more frequent information is needed, it needs to be saved more frequently. -Justin El 18/10/12 18:09, Nilesh Dhumal escribió: Hello, I am calculating the dipole moment auto-correlation function for my system which have 128 cation and 128 anion. I am saving the trajectory at each 2 ps and using this trajectory for further analysis. Can I save the dipole moment and three vectors at each 3 fs? Thanks Nilesh -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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 -- Javier CEREZO BASTIDA Ph.D. Student Physical Chemistry Universidad de Murcia 30100, Murcia (SPAIN) T: (0034)868887434 -- 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 -- Javier CEREZO BASTIDA PhD Student Physical Chemistry Universidad de Murcia Murcia (Spain) Tel: (+34)868887434 -- 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] Dipole moment
Dear Gromacs, I am trying to install gromacs with mpi enabled in my cluster and i end up with following error: libtool: link: cannot find the library `../mdlib/libmd_mpi.la' or unhandled argument `../mdlib/libmd_mpi.la' make[1]: *** [libgmxpreprocess_mpi.la] Error I can able to install gromacs in single precision without having trouble. However, when i use mpi enabled by using lam-7.4.1 it gives above mentioned error, I have tried openmpi also but its not even compile it and ends up with error like configure: error: cannot compute sizeof (off_t) I have used the command line ./configure --program-suffix=_mpi --enable-mpi --enable-shared I do not know how to solve this problem. Any suggestion would be much appreciated. Regards Rajiv On Fri, Oct 19, 2012 at 4:17 PM, Javier Cerezo j...@um.es wrote: When calculated during the md run, the corresponding options in g_energy for the dipole moment are MU-X, MU-Y and MU-Z. However, taking into account the previous mail by David van der Spoel, it's possible that the dipole moment could not be calculated in your system. Options in g_energy vary depending on the actual computation. If you want to calculate the dipole moment by your own, I think it's easier to use the xtc file exported every 3fs (it'll be considerably heavier than the edr file, however) and writing an specific code for your purposes. In order to read the trajectories, you can use the xtc library ( http://www.gromacs.org/**Developer_Zone/Programming_**Guide/XTC_Libraryhttp://www.gromacs.org/Developer_Zone/Programming_Guide/XTC_Library). Anyway, if the code didn't compute it, there should be a reason. Javier El 19/10/12 04:42, Nilesh Dhumal escribió: Is it possible to calcualte the dipole moment at 3fs by modifing the source code? Nilesh How can I save the total dipole moment extacted by .edr file? I could not find the option in g_energy. Nilesh Justin is right. I've slipped a bit, that was not the way to set nstenergy. But still, you can save the dipole directly in the edr file. Not from your existing trajectory, but in a new run. Say your dt=1fs, then you should set nstenergy=3 to get your dipole moment every 3fs which you can retrieve with g_energy. Javier El 18/10/12 20:43, Nilesh Dhumal escribió: In short, I can not save dipole moment directly. I can calculate dipole moment only using .trr file. Nilesh On 10/18/12 1:45 PM, Javier Cerezo wrote: Hi The dipole is stored in the edr file, which output frequency is controlled by nstenergy option in the mdp parameter file. Set it appropriately during your run (nstenergy=0.003) but keep in mind that it should be a multiple of the time step. nstenergy cannot be set this way; it is an integer indicating the interval (in number of steps) for writing energy values. If the values have been saved every 2 ps, there is no way to retrieve them every 3 fs; if more frequent information is needed, it needs to be saved more frequently. -Justin El 18/10/12 18:09, Nilesh Dhumal escribió: Hello, I am calculating the dipole moment auto-correlation function for my system which have 128 cation and 128 anion. I am saving the trajectory at each 2 ps and using this trajectory for further analysis. Can I save the dipole moment and three vectors at each 3 fs? Thanks Nilesh -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/**Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://www.gromacs.org/Support/Mailing_Lists -- Javier CEREZO BASTIDA Ph.D. Student Physical Chemistry Universidad de Murcia 30100, Murcia (SPAIN) T: (0034)868887434 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/**Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list
Re: [gmx-users] Dipole moment
Dear Rajiv, Please start a different thread, if you want to get help. I suppose you need to be informative regarding your error(s). Chandan -- Chandan kumar Choudhury NCL, Pune INDIA On Fri, Oct 19, 2012 at 2:07 PM, Rajiv Gandhi graji...@gmail.com wrote: Dear Gromacs, I am trying to install gromacs with mpi enabled in my cluster and i end up with following error: libtool: link: cannot find the library `../mdlib/libmd_mpi.la' or unhandled argument `../mdlib/libmd_mpi.la' make[1]: *** [libgmxpreprocess_mpi.la] Error I can able to install gromacs in single precision without having trouble. However, when i use mpi enabled by using lam-7.4.1 it gives above mentioned error, I have tried openmpi also but its not even compile it and ends up with error like configure: error: cannot compute sizeof (off_t) I have used the command line ./configure --program-suffix=_mpi --enable-mpi --enable-shared I do not know how to solve this problem. Any suggestion would be much appreciated. Regards Rajiv On Fri, Oct 19, 2012 at 4:17 PM, Javier Cerezo j...@um.es wrote: When calculated during the md run, the corresponding options in g_energy for the dipole moment are MU-X, MU-Y and MU-Z. However, taking into account the previous mail by David van der Spoel, it's possible that the dipole moment could not be calculated in your system. Options in g_energy vary depending on the actual computation. If you want to calculate the dipole moment by your own, I think it's easier to use the xtc file exported every 3fs (it'll be considerably heavier than the edr file, however) and writing an specific code for your purposes. In order to read the trajectories, you can use the xtc library ( http://www.gromacs.org/**Developer_Zone/Programming_**Guide/XTC_Libraryhttp://www.gromacs.org/Developer_Zone/Programming_Guide/XTC_Library). Anyway, if the code didn't compute it, there should be a reason. Javier El 19/10/12 04:42, Nilesh Dhumal escribió: Is it possible to calcualte the dipole moment at 3fs by modifing the source code? Nilesh How can I save the total dipole moment extacted by .edr file? I could not find the option in g_energy. Nilesh Justin is right. I've slipped a bit, that was not the way to set nstenergy. But still, you can save the dipole directly in the edr file. Not from your existing trajectory, but in a new run. Say your dt=1fs, then you should set nstenergy=3 to get your dipole moment every 3fs which you can retrieve with g_energy. Javier El 18/10/12 20:43, Nilesh Dhumal escribió: In short, I can not save dipole moment directly. I can calculate dipole moment only using .trr file. Nilesh On 10/18/12 1:45 PM, Javier Cerezo wrote: Hi The dipole is stored in the edr file, which output frequency is controlled by nstenergy option in the mdp parameter file. Set it appropriately during your run (nstenergy=0.003) but keep in mind that it should be a multiple of the time step. nstenergy cannot be set this way; it is an integer indicating the interval (in number of steps) for writing energy values. If the values have been saved every 2 ps, there is no way to retrieve them every 3 fs; if more frequent information is needed, it needs to be saved more frequently. -Justin El 18/10/12 18:09, Nilesh Dhumal escribió: Hello, I am calculating the dipole moment auto-correlation function for my system which have 128 cation and 128 anion. I am saving the trajectory at each 2 ps and using this trajectory for further analysis. Can I save the dipole moment and three vectors at each 3 fs? Thanks Nilesh -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/**Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://www.gromacs.org/Support/Mailing_Lists -- Javier CEREZO BASTIDA Ph.D. Student Physical Chemistry Universidad de Murcia 30100, Murcia (SPAIN) T: (0034)868887434 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/**Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting!
[gmx-users] Dipole moment
Hello, I am calculating the dipole moment auto-correlation function for my system which have 128 cation and 128 anion. I am saving the trajectory at each 2 ps and using this trajectory for further analysis. Can I save the dipole moment and three vectors at each 3 fs? 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] Dipole moment
Hi The dipole is stored in the edr file, which output frequency is controlled by nstenergy option in the mdp parameter file. Set it appropriately during your run (nstenergy=0.003) but keep in mind that it should be a multiple of the time step. Javier El 18/10/12 18:09, Nilesh Dhumal escribió: Hello, I am calculating the dipole moment auto-correlation function for my system which have 128 cation and 128 anion. I am saving the trajectory at each 2 ps and using this trajectory for further analysis. Can I save the dipole moment and three vectors at each 3 fs? Thanks Nilesh -- Javier CEREZO BASTIDA Ph.D. Student Physical Chemistry Universidad de Murcia 30100, Murcia (SPAIN) T: (0034)868887434 -- 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] Dipole moment
On 10/18/12 1:45 PM, Javier Cerezo wrote: Hi The dipole is stored in the edr file, which output frequency is controlled by nstenergy option in the mdp parameter file. Set it appropriately during your run (nstenergy=0.003) but keep in mind that it should be a multiple of the time step. nstenergy cannot be set this way; it is an integer indicating the interval (in number of steps) for writing energy values. If the values have been saved every 2 ps, there is no way to retrieve them every 3 fs; if more frequent information is needed, it needs to be saved more frequently. -Justin El 18/10/12 18:09, Nilesh Dhumal escribió: Hello, I am calculating the dipole moment auto-correlation function for my system which have 128 cation and 128 anion. I am saving the trajectory at each 2 ps and using this trajectory for further analysis. Can I save the dipole moment and three vectors at each 3 fs? Thanks Nilesh -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] Dipole moment
On 2012-10-18 18:09, Nilesh Dhumal wrote: Hello, I am calculating the dipole moment auto-correlation function for my system which have 128 cation and 128 anion. I am saving the trajectory at each 2 ps and using this trajectory for further analysis. Can I save the dipole moment and three vectors at each 3 fs? The dipole moment of charged box is not defined, since if one ion hops over periodic boundary conditions to the next box the dipole makes an enormous jump. 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] Dipole moment
In short, I can save dipole moment with the same frequency, the trajectory save. Nilesh On 10/18/12 1:45 PM, Javier Cerezo wrote: Hi The dipole is stored in the edr file, which output frequency is controlled by nstenergy option in the mdp parameter file. Set it appropriately during your run (nstenergy=0.003) but keep in mind that it should be a multiple of the time step. nstenergy cannot be set this way; it is an integer indicating the interval (in number of steps) for writing energy values. If the values have been saved every 2 ps, there is no way to retrieve them every 3 fs; if more frequent information is needed, it needs to be saved more frequently. -Justin El 18/10/12 18:09, Nilesh Dhumal escribió: Hello, I am calculating the dipole moment auto-correlation function for my system which have 128 cation and 128 anion. I am saving the trajectory at each 2 ps and using this trajectory for further analysis. Can I save the dipole moment and three vectors at each 3 fs? Thanks Nilesh -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] Dipole moment
In short, I can not save dipole moment directly. I can calculate dipole moment only using .trr file. Nilesh On 10/18/12 1:45 PM, Javier Cerezo wrote: Hi The dipole is stored in the edr file, which output frequency is controlled by nstenergy option in the mdp parameter file. Set it appropriately during your run (nstenergy=0.003) but keep in mind that it should be a multiple of the time step. nstenergy cannot be set this way; it is an integer indicating the interval (in number of steps) for writing energy values. If the values have been saved every 2 ps, there is no way to retrieve them every 3 fs; if more frequent information is needed, it needs to be saved more frequently. -Justin El 18/10/12 18:09, Nilesh Dhumal escribió: Hello, I am calculating the dipole moment auto-correlation function for my system which have 128 cation and 128 anion. I am saving the trajectory at each 2 ps and using this trajectory for further analysis. Can I save the dipole moment and three vectors at each 3 fs? Thanks Nilesh -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] Dipole moment
Justin is right. I've slipped a bit, that was not the way to set nstenergy. But still, you can save the dipole directly in the edr file. Not from your existing trajectory, but in a new run. Say your dt=1fs, then you should set nstenergy=3 to get your dipole moment every 3fs which you can retrieve with g_energy. Javier El 18/10/12 20:43, Nilesh Dhumal escribió: In short, I can not save dipole moment directly. I can calculate dipole moment only using .trr file. Nilesh On 10/18/12 1:45 PM, Javier Cerezo wrote: Hi The dipole is stored in the edr file, which output frequency is controlled by nstenergy option in the mdp parameter file. Set it appropriately during your run (nstenergy=0.003) but keep in mind that it should be a multiple of the time step. nstenergy cannot be set this way; it is an integer indicating the interval (in number of steps) for writing energy values. If the values have been saved every 2 ps, there is no way to retrieve them every 3 fs; if more frequent information is needed, it needs to be saved more frequently. -Justin El 18/10/12 18:09, Nilesh Dhumal escribió: Hello, I am calculating the dipole moment auto-correlation function for my system which have 128 cation and 128 anion. I am saving the trajectory at each 2 ps and using this trajectory for further analysis. Can I save the dipole moment and three vectors at each 3 fs? Thanks Nilesh -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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 -- Javier CEREZO BASTIDA Ph.D. Student Physical Chemistry Universidad de Murcia 30100, Murcia (SPAIN) T: (0034)868887434 -- 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] Dipole moment
How can I save the total dipole moment extacted by .edr file? I could not find the option in g_energy. Nilesh Justin is right. I've slipped a bit, that was not the way to set nstenergy. But still, you can save the dipole directly in the edr file. Not from your existing trajectory, but in a new run. Say your dt=1fs, then you should set nstenergy=3 to get your dipole moment every 3fs which you can retrieve with g_energy. Javier El 18/10/12 20:43, Nilesh Dhumal escribió: In short, I can not save dipole moment directly. I can calculate dipole moment only using .trr file. Nilesh On 10/18/12 1:45 PM, Javier Cerezo wrote: Hi The dipole is stored in the edr file, which output frequency is controlled by nstenergy option in the mdp parameter file. Set it appropriately during your run (nstenergy=0.003) but keep in mind that it should be a multiple of the time step. nstenergy cannot be set this way; it is an integer indicating the interval (in number of steps) for writing energy values. If the values have been saved every 2 ps, there is no way to retrieve them every 3 fs; if more frequent information is needed, it needs to be saved more frequently. -Justin El 18/10/12 18:09, Nilesh Dhumal escribió: Hello, I am calculating the dipole moment auto-correlation function for my system which have 128 cation and 128 anion. I am saving the trajectory at each 2 ps and using this trajectory for further analysis. Can I save the dipole moment and three vectors at each 3 fs? Thanks Nilesh -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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 -- Javier CEREZO BASTIDA Ph.D. Student Physical Chemistry Universidad de Murcia 30100, Murcia (SPAIN) T: (0034)868887434 -- 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] Dipole moment
Is it possible to calcualte the dipole moment at 3fs by modifing the source code? Nilesh How can I save the total dipole moment extacted by .edr file? I could not find the option in g_energy. Nilesh Justin is right. I've slipped a bit, that was not the way to set nstenergy. But still, you can save the dipole directly in the edr file. Not from your existing trajectory, but in a new run. Say your dt=1fs, then you should set nstenergy=3 to get your dipole moment every 3fs which you can retrieve with g_energy. Javier El 18/10/12 20:43, Nilesh Dhumal escribió: In short, I can not save dipole moment directly. I can calculate dipole moment only using .trr file. Nilesh On 10/18/12 1:45 PM, Javier Cerezo wrote: Hi The dipole is stored in the edr file, which output frequency is controlled by nstenergy option in the mdp parameter file. Set it appropriately during your run (nstenergy=0.003) but keep in mind that it should be a multiple of the time step. nstenergy cannot be set this way; it is an integer indicating the interval (in number of steps) for writing energy values. If the values have been saved every 2 ps, there is no way to retrieve them every 3 fs; if more frequent information is needed, it needs to be saved more frequently. -Justin El 18/10/12 18:09, Nilesh Dhumal escribió: Hello, I am calculating the dipole moment auto-correlation function for my system which have 128 cation and 128 anion. I am saving the trajectory at each 2 ps and using this trajectory for further analysis. Can I save the dipole moment and three vectors at each 3 fs? Thanks Nilesh -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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 -- Javier CEREZO BASTIDA Ph.D. Student Physical Chemistry Universidad de Murcia 30100, Murcia (SPAIN) T: (0034)868887434 -- 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 -- 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] dipole moment of a molecule
On Fri, 2012-05-18 at 09:49 -0700, Milinda Samaraweera wrote: Hi Guys Could you please explain to me how to use the g_dipole method to calculate the dipole moment of a Solute in a solvent. Hi, there has just recently been a discussion on this mailing list. Actually you need just an indexfile that contains a group with the solute atoms. Then you just have to choose this group when you execute g_dipoles. However, you have to check the force field, how the partial charges have been parametrised in order to consider the correct electronic polarization. Furthermore, if the solute is charged, there is no unique dipole moment defined, because it will depend on the choice of the origin. In g_dipoles, the COM is chosen as the reference system, if a molecule is charged. /Flo Thanks alot Milinda Samaraweera University of Connecticut Department of Chemistry 55 N Eagleville road unit 3060 Storrs CT USA -- 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 -- 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
[gmx-users] dipole moment of a molecule
Hi Guys Could you please explain to me how to use the g_dipole method to calculate the dipole moment of a Solute in a solvent. Thanks alot Milinda Samaraweera University of Connecticut Department of Chemistry 55 N Eagleville road unit 3060 Storrs CT USA-- 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] dipole moment
Hi, You do not need to use the polarizable martini water model to calculate the dipole of molecules. Or I am missing a point here! g_dipole should do the work XAvier. On May 13, 2012, at 15:11, dina dusti dinadu...@yahoo.com wrote: Dear Justin, Thank you very much from your response. Best Regards Dina From: Justin A. Lemkul jalem...@vt.edu To: dina dusti dinadu...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Sunday, May 13, 2012 5:23 PM Subject: Re: [gmx-users] dipole moment On 5/13/12 8:41 AM, dina dusti wrote: Dear GROMACS Specialists, I have one system consists of water and two other molecules. I work by MARTINI CG force field. I want to calculate dipole moment of molecules in water. May I ask you to help me, Please? I doubt you can. Unless you are using version 2.P of the force field (which contains polarizable water), MARTINI uses a single, uncharged particle to represent water. If there are no charges, there is no dipole. -Justin -- Justin A. Lemkul, Ph.D. Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] dipole moment
On Mon, 2012-05-14 at 09:59 +0200, XAvier Periole wrote: Hi, You do not need to use the polarizable martini water model to calculate the dipole of molecules. Or I am missing a point here! g_dipole should do the work XAvier. Hi, I want to point to another problem. If you simulate with a classical force field, you usually have an effective set of partial charges. This means polarization effects are often included in the partial charges. This in turn requires an appropriate calculation of the dipoles. A simple sum over the charges, like g_dipole or g_current does, is not sufficient. The true dipoles are only obtained, if the results from the MD are multiplied with a certain factor the is related to the high-frequency limit of the dielectric constant, the electronic dielectric constant. We have performed several studies on molecular ionic liquids and showed, that with a set of bulk charges, the dipole moments are reproduced correctly, if this electronic dielectric constant is taken into account appropriate. Also for water or any other molecule, the same arguments hold. For example, if TIP4P water is considered. Calculating the dielectric constant gives a value around 50, which is small compared to the exp. value of 80. However, if the correct dipoles are considered, a simulated value of around 80 is the result. Hence, it depends on the parametrization of the partial charges, how the dipole moment or any related property has to be calculated. If you are just interested in the static limit, an effective description with static partial charges is sufficient in my opinion. However, as soon as you are also interested in the time behavior, like the frequency spectrum of the dielectric constant or conductivity, you consider the electronic polarization explicitly with a corresponding force field, as Justin mentioned. Cheers, Flo On May 13, 2012, at 15:11, dina dusti dinadu...@yahoo.com wrote: Dear Justin, Thank you very much from your response. Best Regards Dina From: Justin A. Lemkul jalem...@vt.edu To: dina dusti dinadu...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Sunday, May 13, 2012 5:23 PM Subject: Re: [gmx-users] dipole moment On 5/13/12 8:41 AM, dina dusti wrote: Dear GROMACS Specialists, I have one system consists of water and two other molecules. I work by MARTINI CG force field. I want to calculate dipole moment of molecules in water. May I ask you to help me, Please? I doubt you can. Unless you are using version 2.P of the force field (which contains polarizable water), MARTINI uses a single, uncharged particle to represent water. If there are no charges, there is no dipole. -Justin -- Justin A. Lemkul, Ph.D. Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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 -- 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] dipole moment
Interesting ... do you have a reference for this? XAvier. On May 14, 2012, at 12:01 PM, Dommert Florian wrote: On Mon, 2012-05-14 at 09:59 +0200, XAvier Periole wrote: Hi, You do not need to use the polarizable martini water model to calculate the dipole of molecules. Or I am missing a point here! g_dipole should do the work XAvier. Hi, I want to point to another problem. If you simulate with a classical force field, you usually have an effective set of partial charges. This means polarization effects are often included in the partial charges. This in turn requires an appropriate calculation of the dipoles. A simple sum over the charges, like g_dipole or g_current does, is not sufficient. The true dipoles are only obtained, if the results from the MD are multiplied with a certain factor the is related to the high-frequency limit of the dielectric constant, the electronic dielectric constant. We have performed several studies on molecular ionic liquids and showed, that with a set of bulk charges, the dipole moments are reproduced correctly, if this electronic dielectric constant is taken into account appropriate. Also for water or any other molecule, the same arguments hold. For example, if TIP4P water is considered. Calculating the dielectric constant gives a value around 50, which is small compared to the exp. value of 80. However, if the correct dipoles are considered, a simulated value of around 80 is the result. Hence, it depends on the parametrization of the partial charges, how the dipole moment or any related property has to be calculated. If you are just interested in the static limit, an effective description with static partial charges is sufficient in my opinion. However, as soon as you are also interested in the time behavior, like the frequency spectrum of the dielectric constant or conductivity, you consider the electronic polarization explicitly with a corresponding force field, as Justin mentioned. Cheers, Flo On May 13, 2012, at 15:11, dina dusti dinadu...@yahoo.com wrote: Dear Justin, Thank you very much from your response. Best Regards Dina From: Justin A. Lemkul jalem...@vt.edu To: dina dusti dinadu...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Sunday, May 13, 2012 5:23 PM Subject: Re: [gmx-users] dipole moment On 5/13/12 8:41 AM, dina dusti wrote: Dear GROMACS Specialists, I have one system consists of water and two other molecules. I work by MARTINI CG force field. I want to calculate dipole moment of molecules in water. May I ask you to help me, Please? I doubt you can. Unless you are using version 2.P of the force field (which contains polarizable water), MARTINI uses a single, uncharged particle to represent water. If there are no charges, there is no dipole. -Justin -- Justin A. Lemkul, Ph.D. Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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 -- 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? Read http://www.gromacs.org
Re: [gmx-users] dipole moment
On Mon, 2012-05-14 at 12:27 +0200, XAvier Periole wrote: Interesting ... do you have a reference for this? Sure, a detailed discussion about charges for the liquid phase and results for molecular ionic liquids are published in: http://dx.doi.org/10.1039/C1FD00051A and http://pubs.acs.org/doi/abs/10.1021/ct200375v while the theory is based on: http://dx.doi.org/10.1063/1.3060164 and applied to water in: http://pubs.acs.org/doi/abs/10.1021/ct1002048 /Flo XAvier. On May 14, 2012, at 12:01 PM, Dommert Florian wrote: On Mon, 2012-05-14 at 09:59 +0200, XAvier Periole wrote: Hi, You do not need to use the polarizable martini water model to calculate the dipole of molecules. Or I am missing a point here! g_dipole should do the work XAvier. Hi, I want to point to another problem. If you simulate with a classical force field, you usually have an effective set of partial charges. This means polarization effects are often included in the partial charges. This in turn requires an appropriate calculation of the dipoles. A simple sum over the charges, like g_dipole or g_current does, is not sufficient. The true dipoles are only obtained, if the results from the MD are multiplied with a certain factor the is related to the high-frequency limit of the dielectric constant, the electronic dielectric constant. We have performed several studies on molecular ionic liquids and showed, that with a set of bulk charges, the dipole moments are reproduced correctly, if this electronic dielectric constant is taken into account appropriate. Also for water or any other molecule, the same arguments hold. For example, if TIP4P water is considered. Calculating the dielectric constant gives a value around 50, which is small compared to the exp. value of 80. However, if the correct dipoles are considered, a simulated value of around 80 is the result. Hence, it depends on the parametrization of the partial charges, how the dipole moment or any related property has to be calculated. If you are just interested in the static limit, an effective description with static partial charges is sufficient in my opinion. However, as soon as you are also interested in the time behavior, like the frequency spectrum of the dielectric constant or conductivity, you consider the electronic polarization explicitly with a corresponding force field, as Justin mentioned. Cheers, Flo On May 13, 2012, at 15:11, dina dusti dinadu...@yahoo.com wrote: Dear Justin, Thank you very much from your response. Best Regards Dina From: Justin A. Lemkul jalem...@vt.edu To: dina dusti dinadu...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Sunday, May 13, 2012 5:23 PM Subject: Re: [gmx-users] dipole moment On 5/13/12 8:41 AM, dina dusti wrote: Dear GROMACS Specialists, I have one system consists of water and two other molecules. I work by MARTINI CG force field. I want to calculate dipole moment of molecules in water. May I ask you to help me, Please? I doubt you can. Unless you are using version 2.P of the force field (which contains polarizable water), MARTINI uses a single, uncharged particle to represent water. If there are no charges, there is no dipole. -Justin -- Justin A. Lemkul, Ph.D. Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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 -- 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
[gmx-users] dipole moment
Dear GROMACS Specialists, I have one system consists of water and two other molecules. I work by MARTINI CG force field. I want to calculate dipole moment of molecules in water. May I ask you to help me, Please? Best Regards Dina -- 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] dipole moment
On 5/13/12 8:41 AM, dina dusti wrote: Dear GROMACS Specialists, I have one system consists of water and two other molecules. I work by MARTINI CG force field. I want to calculate dipole moment of molecules in water. May I ask you to help me, Please? I doubt you can. Unless you are using version 2.P of the force field (which contains polarizable water), MARTINI uses a single, uncharged particle to represent water. If there are no charges, there is no dipole. -Justin -- Justin A. Lemkul, Ph.D. Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] dipole moment
Dear Justin, Thank you very much from your response. Best Regards Dina From: Justin A. Lemkul jalem...@vt.edu To: dina dusti dinadu...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Sunday, May 13, 2012 5:23 PM Subject: Re: [gmx-users] dipole moment On 5/13/12 8:41 AM, dina dusti wrote: Dear GROMACS Specialists, I have one system consists of water and two other molecules. I work by MARTINI CG force field. I want to calculate dipole moment of molecules in water. May I ask you to help me, Please? I doubt you can. Unless you are using version 2.P of the force field (which contains polarizable water), MARTINI uses a single, uncharged particle to represent water. If there are no charges, there is no dipole. -Justin -- Justin A. Lemkul, Ph.D. Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] dipole moment
I want to see the change in dipole moment alond the simulation. NIlesh On Wed, May 25, 2011 11:32 am, David van der Spoel wrote: On 2011-05-25 17.14, Nilesh Dhumal wrote: Hello, Can I calculate a dipole moment of a particular bond? It is easier to do it manually. Otherwise g_dipoles with a suitable index file would do it. The sum of charges has to be zero of course. I am using gromacs version 4.0.7. 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] dipole moment
Thanks for reply. Here are more details about my simulation. I have glucose molecule in my system. I am interested in change in dipole moment of OH bond of glucose along the simulation. I have made the index file. How can I select two groups (oxygen and hydrogen) or should I put particular oxygen and hydrogen in same group (manually). Nilesh On Wed, May 25, 2011 11:59 am, David van der Spoel wrote: On 2011-05-25 17.36, Nilesh Dhumal wrote: I want to see the change in dipole moment alond the simulation. g_dipoles -h NIlesh On Wed, May 25, 2011 11:32 am, David van der Spoel wrote: On 2011-05-25 17.14, Nilesh Dhumal wrote: Hello, Can I calculate a dipole moment of a particular bond? It is easier to do it manually. Otherwise g_dipoles with a suitable index file would do it. The sum of charges has to be zero of course. I am using gromacs version 4.0.7. 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 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] dipole moment
On 2011-05-25 18.03, Nilesh Dhumal wrote: Thanks for reply. Here are more details about my simulation. I have glucose molecule in my system. I am interested in change in dipole moment of OH bond of glucose along the simulation. The OH group is not neutral so your dipole is meaningless (position dependent). Otherwise the charges are constant and the fluctuation in bond length (if you have a flexible molecule) will be small, or zero with constraints. You should think what you want to get out. What experiment you want to compare to. I have made the index file. How can I select two groups (oxygen and hydrogen) or should I put particular oxygen and hydrogen in same group (manually). Nilesh On Wed, May 25, 2011 11:59 am, David van der Spoel wrote: On 2011-05-25 17.36, Nilesh Dhumal wrote: I want to see the change in dipole moment alond the simulation. g_dipoles -h NIlesh On Wed, May 25, 2011 11:32 am, David van der Spoel wrote: On 2011-05-25 17.14, Nilesh Dhumal wrote: Hello, Can I calculate a dipole moment of a particular bond? It is easier to do it manually. Otherwise g_dipoles with a suitable index file would do it. The sum of charges has to be zero of course. I am using gromacs version 4.0.7. 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 -- 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] dipole moment
Basically I want to calculate the stretching vibration of the bond by fourier transfrom of dipole momenet autocorrelation fucntion or velocity autocorrelation function. Before going for vibration I wanted to check the fluctuation of dipole moment along the simulation. Can I calculate the velocity autocorrelation function for a bond. Nilesh On Wed, May 25, 2011 12:37 pm, David van der Spoel wrote: On 2011-05-25 18.03, Nilesh Dhumal wrote: Thanks for reply. Here are more details about my simulation. I have glucose molecule in my system. I am interested in change in dipole moment of OH bond of glucose along the simulation. The OH group is not neutral so your dipole is meaningless (position dependent). Otherwise the charges are constant and the fluctuation in bond length (if you have a flexible molecule) will be small, or zero with constraints. You should think what you want to get out. What experiment you want to compare to. I have made the index file. How can I select two groups (oxygen and hydrogen) or should I put particular oxygen and hydrogen in same group (manually). Nilesh On Wed, May 25, 2011 11:59 am, David van der Spoel wrote: On 2011-05-25 17.36, Nilesh Dhumal wrote: I want to see the change in dipole moment alond the simulation. g_dipoles -h NIlesh On Wed, May 25, 2011 11:32 am, David van der Spoel wrote: On 2011-05-25 17.14, Nilesh Dhumal wrote: Hello, Can I calculate a dipole moment of a particular bond? It is easier to do it manually. Otherwise g_dipoles with a suitable index file would do it. The sum of charges has to be zero of course. I am using gromacs version 4.0.7. 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 -- 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] dipole moment
On 2011-05-25 20.42, Nilesh Dhumal wrote: Basically I want to calculate the stretching vibration of the bond by fourier transfrom of dipole momenet autocorrelation fucntion or velocity autocorrelation function. Before going for vibration I wanted to check the fluctuation of dipole moment along the simulation. Can I calculate the velocity autocorrelation function for a bond. Of course. How about g_velacc Nilesh On Wed, May 25, 2011 12:37 pm, David van der Spoel wrote: On 2011-05-25 18.03, Nilesh Dhumal wrote: Thanks for reply. Here are more details about my simulation. I have glucose molecule in my system. I am interested in change in dipole moment of OH bond of glucose along the simulation. The OH group is not neutral so your dipole is meaningless (position dependent). Otherwise the charges are constant and the fluctuation in bond length (if you have a flexible molecule) will be small, or zero with constraints. You should think what you want to get out. What experiment you want to compare to. I have made the index file. How can I select two groups (oxygen and hydrogen) or should I put particular oxygen and hydrogen in same group (manually). Nilesh On Wed, May 25, 2011 11:59 am, David van der Spoel wrote: On 2011-05-25 17.36, Nilesh Dhumal wrote: I want to see the change in dipole moment alond the simulation. g_dipoles -h NIlesh On Wed, May 25, 2011 11:32 am, David van der Spoel wrote: On 2011-05-25 17.14, Nilesh Dhumal wrote: Hello, Can I calculate a dipole moment of a particular bond? It is easier to do it manually. Otherwise g_dipoles with a suitable index file would do it. The sum of charges has to be zero of course. I am using gromacs version 4.0.7. Thanks Nilesh -- David van der Spoel, Ph.D., Professor of Biology Dept. of CellMolec. 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 -- 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
Re: [gmx-users] dipole moment of a charged peptide
On Thu, 2011-03-31 at 18:03 -0700, Sanku M wrote: Hi, I have a long-chain peptide which has a net charge of +5 . I was wondering whether the g_dipole will give any reasonable dipole moment for a molecule with a net charge. Is there any suggestion I should follow regarding calculation of dipole-moment of a charged molecule . I found that in the manual it is mentioned that 'For molecules with a net charge, the net charge is subtracted atcenter of mass of the molecule.'. I did not understand what it means. I am using gromacs-4.0.7. Sanku If you have a charged molecule the dipole moment is not unique, so you have to choose a reference point and this can be done by subtracting the net charge at this point. Write down the formula and rearange the terms and you will clearly see, what I mean. Cheers, Flo -- 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 -- 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] dipole moment of a charged peptide
Dommert Florian skrev 2011-04-01 09.45: On Thu, 2011-03-31 at 18:03 -0700, Sanku M wrote: Hi, I have a long-chain peptide which has a net charge of +5 . I was wondering whether the g_dipole will give any reasonable dipole moment for a molecule with a net charge. Is there any suggestion I should follow regarding calculation of dipole-moment of a charged molecule . I found that in the manual it is mentioned that 'For molecules with a net charge, the net charge is subtracted atcenter of mass of the molecule.'. I did not understand what it means. I am using gromacs-4.0.7. Sanku If you have a charged molecule the dipole moment is not unique, so you have to choose a reference point and this can be done by subtracting the net charge at this point. Write down the formula and rearange the terms and you will clearly see, what I mean. Cheers, Flo And, if I recall correctly, there are two natural choices for this reference pont. One is the center of charge, the other is the center of mass. The latter is perhaps less intuitive, but better related to experimental observables. Erik -- 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 -- --- Erik Marklund, PhD student Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 4537fax: +46 18 511 755 er...@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] dipole moment of a charged peptide
On Fri, 2011-04-01 at 09:48 +0200, Erik Marklund wrote: Dommert Florian skrev 2011-04-01 09.45: On Thu, 2011-03-31 at 18:03 -0700, Sanku M wrote: Hi, I have a long-chain peptide which has a net charge of +5 . I was wondering whether the g_dipole will give any reasonable dipole moment for a molecule with a net charge. Is there any suggestion I should follow regarding calculation of dipole-moment of a charged molecule . I found that in the manual it is mentioned that 'For molecules with a net charge, the net charge is subtracted atcenter of mass of the molecule.'. I did not understand what it means. I am using gromacs-4.0.7. Sanku If you have a charged molecule the dipole moment is not unique, so you have to choose a reference point and this can be done by subtracting the net charge at this point. Write down the formula and rearange the terms and you will clearly see, what I mean. Cheers, Flo And, if I recall correctly, there are two natural choices for this reference pont. One is the center of charge, the other is the center of mass. The latter is perhaps less intuitive, but better related to experimental observables. If you choose the center of charge as reference point, then your molecular dipole moment will be zero, because the dipole moment for a charged molecule can be rewritten as: mu=qtot(x_coq-x_ref) /Flo Erik -- 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 -- 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
[gmx-users] dipole moment of a charged peptide
Hi, I have a long-chain peptide which has a net charge of +5 . I was wondering whether the g_dipole will give any reasonable dipole moment for a molecule with a net charge. Is there any suggestion I should follow regarding calculation of dipole-moment of a charged molecule . I found that in the manual it is mentioned that 'For molecules with a net charge, the net charge is subtracted atcenter of mass of the molecule.'. I did not understand what it means. I am using gromacs-4.0.7. Sanku -- 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] 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 200 ps. 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 value really high (dipcorr.xvg). I pasted some of them. Is there anything wrong or the values are high becuase its not normalized. Thanks Nilesh 0.000 4619.40918 0.001 4619.04248 0.002 4617.97412 0.003 4616.21973 0.004 4613.80176 99.997 -121.73769 99.998 -121.75319 99.999 -121.77924 100.000 -121.81487 -- 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] dipole moment
On 2011-01-25 14.51, Olga Ivchenko wrote: Dear gromacs users, I would like to ask if there is a possibility in gromacs to calculate dipole moment between two atoms. For example one from water and another one from ligand. best, Olga If you mean the combined dipole moment of a particular water and a ligand then you can do it with g_dipoles and an index file. -- 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] dipole moment
Dear David, I mean a dipole moment between a particle atom in a ligand and a particular atom in water molecule. G_dipoles works for molecules, as I understood, not for atoms. best, Olga 2011/1/25 David van der Spoel sp...@xray.bmc.uu.se On 2011-01-25 14.51, Olga Ivchenko wrote: Dear gromacs users, I would like to ask if there is a possibility in gromacs to calculate dipole moment between two atoms. For example one from water and another one from ligand. best, Olga If you mean the combined dipole moment of a particular water and a ligand then you can do it with g_dipoles and an index file. -- 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] dipole moment
On 2011-01-25 16.01, Olga Ivchenko wrote: Dear David, I mean a dipole moment between a particle atom in a ligand and a particular atom in water molecule. G_dipoles works for molecules, as I understood, not for atoms. You can measure the distance between them, the dipole moment will be ill-defined unless the two atoms together have a zero charge. best, Olga 2011/1/25 David van der Spoel sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se On 2011-01-25 14.51, Olga Ivchenko wrote: Dear gromacs users, I would like to ask if there is a possibility in gromacs to calculate dipole moment between two atoms. For example one from water and another one from ligand. best, Olga If you mean the combined dipole moment of a particular water and a ligand then you can do it with g_dipoles and an index file. -- 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/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 mailto: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
Re: [gmx-users] dipole moment
Thank you David, Olga 2011/1/25 David van der Spoel sp...@xray.bmc.uu.se On 2011-01-25 16.01, Olga Ivchenko wrote: Dear David, I mean a dipole moment between a particle atom in a ligand and a particular atom in water molecule. G_dipoles works for molecules, as I understood, not for atoms. You can measure the distance between them, the dipole moment will be ill-defined unless the two atoms together have a zero charge. best, Olga 2011/1/25 David van der Spoel sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se On 2011-01-25 14.51, Olga Ivchenko wrote: Dear gromacs users, I would like to ask if there is a possibility in gromacs to calculate dipole moment between two atoms. For example one from water and another one from ligand. best, Olga If you mean the combined dipole moment of a particular water and a ligand then you can do it with g_dipoles and an index file. -- 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/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 mailto: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 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] dipole moment of molecule of trans and cis azobenzene ?
Hi The partial charges of the trans and cis azobenzene are given as point charges lied on each atom center in my MD simulation. It is supposed that the real molecule of trans-azobenzene has a lower dipole moment than the cis one. So, the real molecule of trans-azobenzene is supposed to be more hydrophobic than the cis one. However, in my MD simulation = The partial charges of the trans and cis azobenzene are given as point charges lied on each atom center. = Is my trans-azobenzene molecule structure more hydrophobic than the cis-one? = how can I calculate the dipole moment from the given partial charges for each atom? Thank you Lin -- 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] dipole moment of molecule of trans and cis azobenzene ?
On 2010-08-26 18.59, Chih-Ying Lin wrote: Hi The partial charges of the trans and cis azobenzene are given as point charges lied on each atom center in my MD simulation. and where do you get the charges from? It is supposed that the real molecule of trans-azobenzene has a lower dipole moment than the cis one. So, the real molecule of trans-azobenzene is supposed to be more hydrophobic than the cis one. However, in my MD simulation = The partial charges of the trans and cis azobenzene are given as point charges lied on each atom center. = Is my trans-azobenzene molecule structure more hydrophobic than the cis-one? = how can I calculate the dipole moment from the given partial charges for each atom? mu = sum_i q r Or g_dipoles. Thank you Lin -- 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
[gmx-users] dipole moment of molecule of trans and cis azobenzene ?
HI The charges of azobenzene from the authors, who made the QM/MM simulations and fit some experimental data about the azobenzene. Thank you Lin On 2010-08-26 18.59, Chih-Ying Lin wrote: Hi The partial charges of the trans and cis azobenzene are given as point charges lied on each atom center in my MD simulation. and where do you get the charges from? It is supposed that the real molecule of trans-azobenzene has a lower dipole moment than the cis one. So, the real molecule of trans-azobenzene is supposed to be more hydrophobic than the cis one. However, in my MD simulation = The partial charges of the trans and cis azobenzene are given as point charges lied on each atom center. = Is my trans-azobenzene molecule structure more hydrophobic than the cis-one? = how can I calculate the dipole moment from the given partial charges for each atom? mu = sum_i q r Or g_dipoles. Thank you Lin -- 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] dipole moment of molecule of trans and cis azobenzene ?
HI From David = dipole moment = mu = sum_i q r. is that sum of partial charges * r ? what is the r ? Thank you Lin On 2010-08-26 18.59, Chih-Ying Lin wrote: Hi The partial charges of the trans and cis azobenzene are given as point charges lied on each atom center in my MD simulation. and where do you get the charges from? It is supposed that the real molecule of trans-azobenzene has a lower dipole moment than the cis one. So, the real molecule of trans-azobenzene is supposed to be more hydrophobic than the cis one. However, in my MD simulation = The partial charges of the trans and cis azobenzene are given as point charges lied on each atom center. = Is my trans-azobenzene molecule structure more hydrophobic than the cis-one? = how can I calculate the dipole moment from the given partial charges for each atom? mu = sum_i q r Or g_dipoles. Thank you Lin -- 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
