[gmx-users] Re: g_velacc

[Nilesh Dhumal]

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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