[gmx-users] Re: g_velacc

[Vitaly Chaban]

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 <ndhumal at 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 <ndhumal at 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
>>>> --
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>>
>>
>
>
>



-- 
Dr. Vitaly V. Chaban, Department of Chemistry
University of Rochester, Rochester, New York 14627-0216