How can I calculate the velocity autocorrelation function of a bond with Gromacs?
Nilesh On Fri, May 27, 2011 8:32 am, Vitaly Chaban wrote: > 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 <ndhu...@andrew.cmu.edu> > 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 >>> <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 >>>>> >>>>> >>> >>> >> >> >> > > > > -- > 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_Lists