It does not change the situation, I believe. What is the sense of calculating such ACF? In order to understand the cross-correlation between the bonded atoms? It will be huge as I understand.
-- Dr. Vitaly V. Chaban, Department of Chemistry University of Rochester, Rochester, New York 14627-0216 On Fri, May 27, 2011 at 8:07 AM, Nilesh Dhumal <ndhu...@andrew.cmu.edu> wrote: > 20 is hydrogen atom. > Sorry its typing mistake. > > Nilesh > > On Fri, May 27, 2011 3:52 am, Vitaly Chaban 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 >>> >>> >>> 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? >> >> >> >> The program acts as if your hydrogen and oxygen are identical atoms. >> >> >> >> -- >> Dr. Vitaly V. Chaban, Department of Chemistry >> University of Rochester, Rochester, New York 14627-0216 >> -- >> 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_Lis -- 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
