[AMBER] MD Analysis - Consistency

From: senal dinuka <senal.ichemc.edu.lk>
Date: Sun, 23 Dec 2018 11:40:44 +0530

Dear AMBER Users,

I have been came up with a doubt which seems simple yet I find myself
harassed by it. Hence I am writing this to mailing list. I simulated
several protein-ligand complexes as in different enzyme oriented studies
with different sets of ligands. All the systems were ranging from 200-500
residue count. Each and every system were equilibrated for a 1ns using
pmemd module followed with 120ns production using pmemd.cuda module. 1ns
equilibration was seem to be sufficient given that system was heated prior
to equilibration and density fluctuations were minimal throughout the
period. Yet I find myself with several complexes whose rmsd shows massive
fluctuations throughout the time and those of few which shows otherwise. I
thought of running a couple of nanosecond more (80 ns) for each complex
considering the consistency. And as I was feared systems shown to have
stable rmsd previously seem to ran in to conformation change after about
150ns and complexes in doubt seem to attain stable behavior.
All these analysis and conclusion were based solely on rmsd behavior. What
I would like to know is

   1. Would consistency be a matter on publishing MD results?
   2. Can we rely on rmsd fluctuation as a fact about stability, if not
   what other methods are better?
   3. For analysis of hbond/gbsa how can we chose the frames, considering
   rmsd of ligands fluctuates drastically throughout the time in most case

Thank you
D L Senal Dinuka
Grad.Chem., A.I.Chem.C.
Research Assistant
College of Chemical Sciences
Institute of Chemistry Ceylon
Sri Lanka
+94 77 627 4678
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Received on Sat Dec 22 2018 - 22:30:02 PST
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