Hello,
I believe the units are, in fact, kcal/mol for energy (that is typically the
energy unit amber prints out) and atm for the pressure. However, see my
comments below.
On Mon, May 17, 2010 at 6:08 AM, Asfa Ali <asfa.iisc.gmail.com> wrote:
> Hi,
>
> What are the units of pressure and energy after doing
> perl process_mdout.perl ../polyAT_wat_md1.out ../polyAT_wat_md2.out
> xmgrace summary.PRES
> xmgrace summary.EPTOT summary.EKTOT summary.ETOT
> (http://ambermd.org/tutorials/basic/tutorial1/section5.htm)
>
> Are they in atm and kcal/mol respectively? If so, the values 500 atm &
> 20000
> kcal/mol are too high !!
>
The pressure is not 500 atm. It appears to average around 0 or so (or 1,
it's impossible to distinguish with that scale. The pressure fluctuations
reach 500 occasionally, but the average is where it should be, There has
been a good deal of discussion on the list recently about large pressure
fluctuations, and has been explained by the near-incompressibility of liquid
water. Therefore, large pressure fluctuations (even of this scale), are
completely expected. The density is a better measure of stability in a
constant pressure simulation.
As for the energy, this is absolutely not too large, what makes you say it
is? Keep in mind that an absolute energy is meaningless in a force field.
With so many water molecules having favorably interacting charge-charge
interactions, I would expect that the large percentage of the negative
energy comes from the water-water electrostatic interactions. To push the
point, if you were to run a high-level ab-initio calculation on a small
water cluster, you would likely get an energy far lower than -20 000
(indeed, the energy for a hydrogen atom is known to be -0.5 hartree, which
is about -315 kcal/mol, and this is only a single, non-interacting atom!).
It is only the energy differences that are of any interest in MD simulations
(so you have to look at the fluctuations, not the absolute value). The
fluctuations appear very small, so there is nothing wrong with this data.
All the best,
Jason
> Thanks in advance..
> Asfa.
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Mon May 17 2010 - 07:00:04 PDT
