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_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<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<http://lists.gromacs.org/mailman/listinfo/gmx-users> >>>>>>> * Please search the archive at >>>>>>> http://www.gromacs.org/**Support/Mailing_Lists/Search<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<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<http://lists.gromacs.org/mailman/listinfo/gmx-users> >>>>> * Please search the archive at >>>>> http://www.gromacs.org/**Support/Mailing_Lists/Search<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<http://www.gromacs.org/Support/Mailing_Lists> >>>>> >>>>> >>>>> >>>> -- >>>> gmx-users mailing list gmx-users@gromacs.org >>>> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> >>>> * Please search the archive at >>>> http://www.gromacs.org/**Support/Mailing_Lists/Search<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<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 list gmx-users@gromacs.org >> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> >> * Please search the archive at http://www.gromacs.org/** >> Support/Mailing_Lists/Search<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<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 -- 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