AMBER Archive (2006)

Subject: Re: AMBER: negative T_solv values

From: David A. Case (case_at_scripps.edu)
Date: Wed Feb 15 2006 - 10:18:25 CST

On Wed, Feb 15, 2006, Markus O Kaukonen wrote:
>
> I'm running Amber 8 on i686 linux, protein solvated in water, with
> truncated octahedral box. A set of atoms are restrained
>
> When doing MD with constant pressure Berendsen I get negative
> T_solv in the energy output (T_solute is OK)

Amber 8 no longer makes any distinction between "solute" and "solvent".
The "Temp" value is the temperature of the entire system, and "T_solv" is
just a placeholder for backwards compatibility in the file format. We
should make that be something less scary, like zero, but there is no
need to worry.

Of course, you should generally visualize your trajectories to help gain
confidence that nothing (else) is wrong.

...good luck....dac

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