[gmx-developers] Semantics of acceleration groups.

[David van der Spoel]

ramon at juguete.quim.ucm.es wrote:
> I am not sure if I understand it. Do you mean that
> the velocities stored in state->v[] are effective
> group velocities? Or are the velocities used
> for the scaling, measured relative to the group
> velocities, the effective group velocities?

The accelerations are on all atoms (in acceleration groups). Temperature 
scaling is applied only on "thermal motion", that is, the group velocity 
is subtracted from the velocity of each atom before T-scaling, and 
afterwards it is added back in. In other words, the temperature of a 
group is defined in a moving frame.

> 
> I guess that the acceleration is applied to the group
> velocity, and included in the velocity of each accelerated
> particle. But it is discounted when discounted when 
> evaluating a thermostat or barostat, so that only the
> part of the velocity not contributed by the acceleration
> is used. 
> 
> Am I right?

No see above.
> 
>>> Looking at the code, it seems that the scaling effect of barostats
>>> and thermostat is not applied to the velocity of the accelerating group.
>>> This velocity is discounted before performing any other operation.
>>>
>>> Why?
>> So that you get effective group velocities.
>> This can in principle be used to compute transport properties.
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-- 
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se