[AMBER] some doubts about simulation analysis

From: Mary Varughese <maryvj1985.gmail.com>
Date: Sat, 27 Jun 2015 13:23:28 +0530


I need to clear some concerns;

Is a 50ns simulation a short time scale with respect to DNA ( containing
modified bases)? is there really any need to run simulations over one micro
When i do a 50 ns simulation how can i tell the reason for that time scale.
The backbone rmsd plot shows somewhat stable trajectory. is not it enough.
How can i convince people?

could i give a measurement of the stability of the duplex or trajectory? Is
there any such analysis method to do that? stable backbone rmsd, all
hydrogen bonds retained throughout, backbone dihedrals and puckering within
the range though broadly distributed is not that enough evidence?

When there is enhancement of stacking, Could by any means, can i show the
enhanced stacking. Is there any method. quantitative other than visually?
in AMBER? any energy analysis methods?

On calculating helical parameters on a representative structure, should i
give the parameters for each base-pair/step? is not average value enough. ?
the trajectory obtained through MD , its usual that all the values not
stick to the standard text book values but the average falls in the
required range. Isnt? Some reduction in helical twist upon simulation is
always observed isnt.(so it would deviate from nmr data isnt?)

It wil be really helpful to have some suggestions.

Thanking you

Mary Varughese
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Received on Sat Jun 27 2015 - 01:00:02 PDT
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