Hi Everyone,
I read through my email again this morning I decided that I better add some
more information to make it easier to diagnose the problem.
After two rounds of energy minization (1. solution, 2. full system) I began
the equilibrium simulations by first heating my protein to 300 K over 25000
steps (50 ps) and then applied density over 25000 steps (ntp=1, taup=1.0).
The next step comprised the 1 ns equilibrium simulation as described in the
previous email to make sure that my protein had in fact reached equilibrium
with regards to temp, density, volume, energies etc. As stated, the the
only value that concerned me is the -0.2514 pressure over 1 ns of
simulation.
Best,
Parker
On Mon, Jul 8, 2013 at 8:25 PM, Parker de Waal <Parker.deWaal09.kzoo.edu>wrote:
> Hi AMBER Users!
>
> I just finished a 1 ns equilibrium run and all of my parameters seem to
> have leveled out fine except for pressure which averaged at -0.2514
>
> see equil.out here ->
> https://gist.github.com/ParkerdeWaal/2d3eddd50c27789b77a8
>
> Does this seem acceptable? I was expecting something around 1 atm...
>
> Best,
> Parker
>
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Received on Tue Jul 09 2013 - 05:00:03 PDT
