On Thu, Jul 21, 2016, Stephan Schott wrote:
> I've been doing some simulations using peptides with restraints to maintain
> certain portions of them in close contact (under 15 A). After running some
> steps, the solute drifted away from the center of the box and crossed the
> boundary, point where the restart file was saved. If I try to resume the
> simulations using this restart file, the energy of the system overflows. It
> seems like pmemd.cuda is calculating the distance before reimaging the
> peptides into the PBC and for what I understand the energy overflow might
> be because of the initial force applied to the restraints.
It's hard to know exactly what is going on from this brief description, but
be sure that iwrap=0 in your simulation -- in this circumstance, you don't
want any imaging.
> First steps after restart:
>
> 0 87.699 13.441
> 5000 ********* *********
Well, for sure, try a run with a much smaller ntpr: you want to find out
what is going on in between step 0 and 5000.
>
> NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
It's odd that the restaint energies are all zero; might be OK, but worth
checking.
....dac
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Received on Fri Jul 22 2016 - 10:00:02 PDT
