[gmx-users] g_velacc

[Nilesh Dhumal]

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.
> spoel at xray.bmc.uu.se    http://folding.bmc.uu.se --
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