[gmx-users] Re: g_velacc

[Nilesh Dhumal]

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

Nilesh



On Fri, May 27, 2011 8:32 am, Vitaly Chaban wrote:
> 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
>
>
>