fix nvt thermostatting

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1

Dear All,
When i read the fix nvt command, it is said in the manual, “The thermostat is applied to only the translational degrees of freedom for the particles. The translational degrees of freedom can also have a bias velocity removed before thermostatting takes place.” and “fix nvt can be used with compute commands that calculate a temperature after removing a “bias” from the atom velocities. E.g. removing the center-of-mass velocity from a group of atoms or only calculating temperature on the x-component of velocity or only calculating temperature for atoms in a geometric region. This is not done by default, but only if the fix_modify command is used to assign a temperature compute to this fix that includes such a bias term. See the doc pages for individual compute commands to determine which ones include a bias. In this case, the thermostat works in the following manner: the current temperature is calculated taking the bias into account, bias is removed from each atom, thermostatting is performed on the remaining thermal degrees of freedom, and the bias is added back in.”
Based on the descriptions above, i am confused by the fllowing commands,

compute mytemp all temp/partial 1 1 0
fix 1 all nvt temp 100 100 0.1
fix_modify 1 temp mytemp
1、At first, in the first line, the temperature compute computes the temperature after excluding the velocity component in z direction.(here is this velocity component in z the bias velocity in nvt thermostatting? )
2、Then this temperature compute style is assigned to the “fix 1 all nvt” by the “fix_modify”. That is, now the “fix 1 all nvt” also calculates the temperature after removing bias velocity(the velocity component in z direction). i’m not sure whether i understand it well.
3、If so, in nvt thermostatting, “the current temperature is calculated taking the bias into account, bias is removed from each atom, thermostatting is performed on the remaining thermal degrees of freedom, and the bias is added back in.”
is this temperature calculate way which takes the bias into consideration inconsistent with the temperature calculate way in 2 which do not take the bias into account?
thank you so much for your answer.

2

The compute command simply measures the temp of the system

using only the xy degrees of freedom. You can access it from

your thermo output or fix ave/time or however you wish.

The fix nvt command thermostats the system. To do this it

by default just used compute temp, to get the global temp of

the system (xyz degrees of freedom = DOF).

But if you use the 3rd command it tells fix nvt to compute its

temp via the temp/partial command. In that case 2 things happen.

The temperature that fix nvt sees is only for the xy DOFs.

And it will only adjust the xy components of velocity to keep

the system at temp=100. It will ignore the z component of velocity.

Steve