[gmx-users] g_velacc

[David van der Spoel]

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
>>>
>>>
>>>
>>>
>>>
>>>
>>
>>
>> --
>> 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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>
>


-- 
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