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

Justin A. Lemkul jalemkul at vt.edu
Thu Jun 14 11:07:57 CEST 2012

On 6/14/12 4:06 AM, ms wrote:
> Ok, I tried some of your suggestions and the Coulomb-SR energies still fall down
> very quickly.
> I wonder if:
> On 13/06/12 16:59, Justin A. Lemkul wrote:
>> 4. What happens when you use the Andersen thermostat? That's not
>> implemented yet for CPU calculations (though it was recently pushed into
>> the 4.6 development branch). Your comment regarding GPU is fine, but I
>> would think grompp would complain.
> maybe mdrun *tries* to use Andersen but since it's not fully implemented for
> CPUs it makes odd artefacts?

The .log file should tell you for sure.  You can also try a different algorithm 
and see if you observe the same behavior.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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