[gmx-users] Re: g_velacc

[Vitaly Chaban]

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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