comparing Classical and Accelerated MD results

From: raghav singh (
Date: Tue Mar 30 2021 - 04:43:00 CDT

Dear NAMD-Users,
I am writing to you all regarding results from Accelerated MD simulations
via NAMD/2.13.
I have a protein(Bovine Beta-casein, 224 aa long), I have generated it's 3D
model using LOMETS, as there is next to zero 3D data available in PDB
regarding the protein as well as no suitable homologs were found using
BLAST search against PDB database.

On the generated model, I have run 1ms of cMD and aMD simulations(RMSD, PCA
and structural information attached). Upon looking at the results, it
appears that in aMD simulations, the protein escapes the starting energy
minima and in full 1ms aMD never revisits the initial conformational space.
Though cMD shows that structural fold is stable in the entirety of the 1ms
simulation time. In my understanding upon smoothening of energy barriers
between different minimas, there should be revisiting/ diffusive events
present in the trajectory!!

I have followed the Amber Accelerated MD tutorial, as well as the following
publications to calculate the aMD parameters for my simulation system.
<;!!DZ3fjg!oTRxImiLTVI5ond7pnNOMYNhctbxm-1msfErThnElf2fpbLduFEkE5JXoMw5vWsqRg$ >*
*2- Hu et al : Revealing the selective mechanisms of inhibitors to PARP-1
and PARP-2 via multiple computational methods
(;!!DZ3fjg!oTRxImiLTVI5ond7pnNOMYNhctbxm-1msfErThnElf2fpbLduFEkE5JXoMxu5rhvwg$ <;!!DZ3fjg!oTRxImiLTVI5ond7pnNOMYNhctbxm-1msfErThnElf2fpbLduFEkE5JXoMxu5rhvwg$ >)*
*3- Gedeon et al : Accelerated molecular dynamics and protein
conformational change: a theoretical and practical guide using a membrane
embedded model neurotransmitter transporter
<;!!DZ3fjg!oTRxImiLTVI5ond7pnNOMYNhctbxm-1msfErThnElf2fpbLduFEkE5JXoMyzHwrjXQ$ >)*

Given that the protein is highly disordered and has a very small percentage
of secondary structure attached to it. Is this behaviour normal ?? or Am I
doing something wrong with my simulation set up??
Most of the structural transitions during the MD are also attached to the
disordered regions of the protein.

Please find the RMSD, RG, PCA and probability histograms and conformational
transition over the course of simulation.;!!DZ3fjg!oTRxImiLTVI5ond7pnNOMYNhctbxm-1msfErThnElf2fpbLduFEkE5JXoMwRn3oLsw$

I would greatly appreciate your help and support to understand if necessary
rectify the problem in my simulations.

Thanking you all for your help and support in advance.


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