[gmx-users] regarding rmsd and gyrate

[rama david]

Hi priya ,

 I am also have same problem...

>From my limited experience ..

To solve these problem it is a good way to make
index file of particular group (or molecule )
and then measure there g_mindist, g_gyrate and g_hbond
You can get gyrate and hbond value for them...
Have a nice Day ...


With Best Wishes,
Ram


On Mon, Apr 9, 2012 at 6:02 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> priya thiyagarajan wrote:
>
>> hello sir ,
>>
>> i got few basic doubts in dynamics..
>>
>> while performing analysis, we are calculating rmsd and gyrate  for single
>> molecule..
>>
>> but in case of more molecules i.e by adding 20 molecules randomly using
>> genbox , when we perform analysis, rmsd value we are obtaining is the
>> average change in structure deviation from initial structure.
>>
>> what about gyrate??
>>
>> i am getting one plot... how to interpret the result for 20
>> moecules..since 20 molecules arranged randomly, how it calculates the
>> gyrate value..
>>
>> please help me with your answer..
>>
>>
> I think g_polystat is more appropriate in this case.
>
> -Justin
>
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