Hi Istvan,
On 23/2/2011, at 1:10 p.m., istvan.kolossvary.hu wrote:
> Ben,
>
> A couple of things that come to mind. Could you run the same molecule
> with AmberTools?
Is it possible to write coordinates out at every step using AmberTools? Also, when you say AmberTools, you're referring more specifically to writing a NAB program, correct?
> If it's OK there it might be an indication that the interface to Sander has recently been broken. The other thing is to
> turn on XMIN verbosity. That way you would have energy and gradient RMS printout from inside XMIN and those number should be the same as in Sander since the same energetic routines compute them.
I had already done so (xmin_verbosity = 2), but hadn't kept the output. So I re-ran the calculation, redirecting output to a file. The energies and RMS gradients in the resulting mdout file match those reported on STDOUT.
> Actually, when you say you see this big discrepancy at the very first step, I wonder if Sander output is simply out of sync and reports the energy before any minimization steps took place.
Yes, and it calls that step 0. At that initial step, the bonding energy term is appropriate for the starting coordinates. At step 1 (i.e., after the first step of minimisation), the energy and coordinates no longer match.
I suspect the problem is with the coordinates, rather than with the energies per se.
Ben
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Received on Wed Feb 23 2011 - 11:00:04 PST
