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

[Justin A. Lemkul]

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

-- 
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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

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