[gmx-users] Strong egative energy drift (losing energy) in explicit water AMBER protein simulation [SOLVED]

[Justin A. Lemkul]

On 6/15/12 6:53 AM, ms wrote:
> Ok, I am using v-rescale now and the major artefacts seem to be gone, at least
> on the very short term (2-3 ns).
>
> It seems grompp should warn that andersen is not a good choice if you're using
> CPUs :)
>

Such a warning would become outdated very soon - the 4.6 development version has 
a proper implementation of the Andersen thermostat.

In the existing code for version 4.5.5, it seems the "Andersen" keyword is 
accepted but there is no mention of its use in update.c or coupling.c, 
suggesting to me that it's a ghost parameter that does nothing.  There should be 
some indication in the .log file that there might be a problem and/or problems 
with the temperature should be apparent.

-Justin

-- 
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================