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? 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 > > > -- 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
