As I said before, g_velacc treats all the atoms in your index file as if they were identical. It does NOT subtract anything.
On Fri, May 27, 2011 at 8:19 AM, Nilesh Dhumal <[email protected]> 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? > > Nilesh > > > On Fri, May 27, 2011 8:11 am, Vitaly Chaban wrote: >> 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 <[email protected]> >> 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 [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_Lis >>>> >> >> > > > -- Dr. Vitaly V. Chaban, Department of Chemistry University of Rochester, Rochester, New York 14627-0216 -- 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
