[AMBER] question of Radius of Gyration

From: Chinh Su Tran To <chinh.sutranto.gmail.com>
Date: Thu, 4 Jul 2013 19:55:38 +0800

Dear AMBER users,

I performed some analyses of radius of gyration, but the result looks
strange to me.
I want to detect how compact my model is, and from there to determine if it
reaches stable conformation (I've already performed Ramachandran plot, RMS
and Energy calculation, and all results show the model is quite stable, but
I wanna analyze the Radius of Gyration to have more insight into this.)

My ptraj file-in is:

*trajin gag_md10ns.mdcrd*
*trajin gag_md20ns.mdcrd
*
*trajin gag_md30ns.mdcrd
*
*trajin gag_md40ns.mdcrd
*
*radgyr out gag_RoG.dat mass*

My "gag_RoG.dat" contains:

*#time RadGyr MaxRad*
* 0.00 41.994157 289.706343*
* 1.00 41.661327 292.020866*
* 2.00 41.672248 291.066736*
* 3.00 41.775243 318.415850*
* 4.00 41.886831 340.357598*
* 5.00 42.010449 328.624739*
* 6.00 42.163676 341.653264*
* 7.00 42.333581 339.423217*
* 8.00 42.499367 334.471394*
* 9.00 42.635248 337.751421*
* 10.00 42.812626 339.781377*
* 11.00 42.920011 330.072199*
* 12.00 43.035933 325.581487*
* 13.00 43.186400 337.890667*
* 14.00 43.380535 347.449550*
* 15.00 43.545429 344.594992*
.....

   *7993.00 286.682822 3487.950027*
* 7994.00 286.548355 3482.219455*
* 7995.00 286.638016 3482.236813*
* 7996.00 286.786611 3493.731442*
* 7997.00 286.748129 3481.676685*
* 7998.00 286.839568 3479.941991*
* 7999.00 286.896013 3482.171648*
* 8000.00 286.775658 3469.712839*

=> Does that mean here the RadGyr is the average values of all the atoms in
the model for each time point (sorry but I am also confused about this time
value, i.e. how long is the interval here!!) ?
Then in this case, how the MaxRad could be interpreted?

Attached is the plot of these RoG values, but it does not seem right to
me!!!

Could you please give some ideas if my ptraj file was wrong?

Thank you.

Regards,
Chinh


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test_RoG.gif
(image/gif attachment: test_RoG.gif)

Received on Thu Jul 04 2013 - 05:00:01 PDT
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