[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.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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