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