On Thu, Jun 10, 2010, Mickey Richards wrote:
> I am comparing the Berendsen thermostat (ntt = 1) to Langevin dynamics (ntt
> = 3), for a long simulation (250 ns) of a carbohydrate in explicit TIP3P
> water in AMBER10, using PMEMD, and GLYCAM06. When I look at the mden file
> generated during my simulations, the temperature for the system and the
> solute are the same, and the temperature for the solvent takes on values of
> -0.2675E+10. These values are similar for both temperature regulation
> schemes.
Amber no longer has any internal idea of what atoms belong to the "solute"
and which ones to the "solvent". I suspect that everything is treated as
solute, which is why solute and system are the same, and that the "solvent"
number is just random garbage left over from earlier code. My comments are
based on sander...Bob may know more about what is going on with pmemd.
....dac
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Received on Thu Jun 10 2010 - 19:00:03 PDT
