[gmx-users] g_velacc

[Nilesh Dhumal]

How can I calculate the velocity autocorrelation function of a bond with
Gromacs?

Nilesh



On Fri, May 27, 2011 8:31 am, David van der Spoel wrote:
> 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 -- gmx-users mailing
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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 --
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