Dear Amber community
I'm attempting to probe the possibility of a conformational change for a 279 residue protein using the dual-boost accelerated Molecular Dynamics.
I used the following to set up the simulations:
residues: 279
atoms: 37887
Ep: -118321
Dihedral energy: 2840 (both base energies taken as averages over a short, standard MD simulation)
alphaD: 3.5 * 279 * 0.25 = 244
ethreshD: 3.5 * 279 + 2840 = 3817
alphaP: 37887 * 0.2 = 7577
ehreshP: -118321 + 7577 = -110744
The issue I encounter is a nearly flat bottom of the dihedral energy curve when plotting it with the added potential (sum of the 4th and 8th column in the amd.log).
Some of the publications I've read on the subject, mention random walks caused by a too high boost to the energy.
Is this also the case for me (in which case I would have to change the settings somehow) or are the simulations "correct" since the total potential energy is not impacted by this behavior ?
Any other comments/observations would also be greatly appreciated.
My thanks for your time.
***
Adam Zalewski
PS: I'm attaching the relevant input and log files below.
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Received on Fri Apr 05 2013 - 05:00:03 PDT
