Re: [AMBER] Amber´14 Solvent box simulation, something went wrong!!

From: Daniel Roe <>
Date: Thu, 4 Aug 2016 09:02:28 -0600

On Thu, Aug 4, 2016 at 3:08 AM, Stregone <> wrote:
> A college said that during the system equilibration, the resulting energies should have
> negative sign. But, since the minimisation, the energy is positive.
> if the I assume that for the equilibration the "zero point" is the energy from the minimisation,
> then the results seem to make sense, as the system heat, then after some time it finds
> a equilibrium.
> But, if in fact the energy should have negative sign, then all is wrong.

Not sure who told you that energies from MD should have a negative
sign, but that's just not true. The absolute value of the energy has
no useful meaning in molecular dynamics simulations (except maybe to
give you a rough idea of the size of your system). What matters are
the *differences* in energy between conformations. I want to make it
completely clear: it doesn't matter if the energy for a given
conformation is positive or negative.

What does strike me as odd about your output is the density (~1.6)
seems quite high. However, since I don't know what you're trying to
simulate I can't really comment further.


Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Thu Aug 04 2016 - 08:30:02 PDT
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