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
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David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell& Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
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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
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