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? 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