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. >>>>> [email protected] http://folding.bmc.uu.se -- 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 >>>>> >>>>> >>>>> >>>>> >>>>> >>>> >>>> >>> >>> >>> -- >>> David van der Spoel, Ph.D., Professor of Biology >>> Dept. of Cell& Molec. Biol., Uppsala University. >>> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. >>> [email protected] http://folding.bmc.uu.se -- 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 >>> >>> >>> >>> >> >> > > > -- > David van der Spoel, Ph.D., Professor of Biology > Dept. of Cell & Molec. Biol., Uppsala University. > Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. > [email protected] http://folding.bmc.uu.se -- > 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
