[AMBER] time scales for running MD

From: Asmita Gupta <asmita4des.gmail.com>
Date: Mon, 1 Sep 2014 16:12:21 +0530

Dear users,

I have carried out an MD simulation using ff12SB(OL3) set of force field on
a RNA riboswitch (26 residues) structure. Instead of doing a very long run,
i decided to perform 3 independent runs for snapshots extracted from
equilibration run (different coordinates and velocities), each of 200ns.

In 2 out of 3 trajectories, the structure is experiencing a loop residue
backbone flipping (zeta, chi and delta), after which it remains stable.
However, with parmbsc0, this residue flipping is not observed at all,
neither with YIL chi correction.

My first doubt is, whether OL3 ffs show any bias towards certain backbone
torsion angle (esp epsilon and zeta) in order to maintain others(chi) and
secondly, is 200ns enough for a good conformational sampling?


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Received on Mon Sep 01 2014 - 04:00:03 PDT
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