[AMBER] Amber and Short Bonds

From: Aronica, Pietro <pietro.aronica07.imperial.ac.uk>
Date: Mon, 26 Mar 2012 15:04:45 +0000

I'm new here, so this is more theoretical than an actual request for help.
I've been dealing with really short bonds, we're talking about less than 0.5 , and Amber, somewhat understandably, is not too pleased with it. My simulations keep failing, and I've changed many parameters around to find out if there's a solution to this. So far, reducing the time step is the only thing that will allow the simulation to reach the conclusion: masses, charges and forces don't seem to have an impact. IS there something I'm overlooking? Or is the timestep the only solution?
I'm mostly using pmemd on a GPU. When my simulations fail, they start displaying NaN as energy values (and restart coordinates). Sometimes they'll go on for a while before failing: visualising in vmd these simulations shows that the short bonds move around very rapidly when compared to the other ones until the whole structure abruptly disappears when the energy goes NaN.
Thanks in advance
Pietro Aronica
Imperial College London
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Received on Mon Mar 26 2012 - 08:30:03 PDT
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