How can I calculate the velocity autocorrelation function of a bond with Gromacs?
Nilesh On Fri, May 27, 2011 8:31 am, David van der Spoel wrote: > On 2011-05-27 14.26, Nilesh Dhumal wrote: > >> I am calculating OH stretching frequency by fourier transform of >> velocity autocorrelation function. >> >> I could calculate the OH stretching frequnecy by calculating fourier >> transform of OH bond. >> >> I want to know how gromacs calculate the velocity autocorrelation >> function of a bond (If I define a bond in index file). >> >> Does is subtract the velocity of hydrogen from oxygen and then >> calculate the autocorrelation function? >> > No, see below! There is no tool that does exactly what you want, however > doing the velacc of just the hydrogen will come close. >> Nilesh >> >> >> >> >> >> On Fri, May 27, 2011 2:37 am, David van der Spoel wrote: >> >>> On 2011-05-26 22.48, Nilesh Dhumal wrote: >>> >>> >>>> Hello, >>>> >>>> >>>> >>>> I have calculated the velocity autocorrelation function of OH bond >>>> in glucose molecule. For this calculation I modified the index file. >>>> The >>>> modified part is pasted below. >>>> >>>> [ O10 ] >>>> 10 20 >>>> >>>> >>> >>> where is the hydrogen? g_velacc knows nothing about bonds just atoms. >>> >>> >>>> >>>> 10 is oxygen no. and 20 is oxygen. >>>> >>>> >>>> >>>> I used following command to calculate the velocity autocorrelation >>>> function. >>>> >>>> g_velacc -f 6.trr -s 6.tpr -n index.ndx -e 100 -nonormalize -o >>>> >>>> >>>> My question is how does the prog. calculate the velocity >>>> autocorrlation function. >>>> >>>> Does is subtract the velocity of hydrogen from oxygen and then >>>> calculate the autocorrelation function? >>>> >>>> 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. >>> sp...@xray.bmc.uu.se http://folding.bmc.uu.se -- 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 >>> >>> >>> >>> >> >> > > > -- > David van der Spoel, Ph.D., Professor of Biology > Dept. of Cell & Molec. Biol., Uppsala University. > Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. > sp...@xray.bmc.uu.se http://folding.bmc.uu.se -- > 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
