[gmx-users] regarding rmsd and gyrate
ramadavidgroup at gmail.com
Mon Apr 9 15:50:29 CEST 2012
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,
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
>> 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 A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
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