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 list 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. >>> * 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 list 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. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > -- gmx-users mailing list 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. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists