Thermostat individual molecules

[MD Simulation]

Hi,

I need to run a simulation of a molecule being shot at a surface.  I'd like to do two things: 1) thermostat the surface and 2) assign a specific velocity to the small molecule.

I see in the MD/THERMOSTAT section, there is a keyword REGION...is this what I would want to do?

If anyone has some ideas, I would appreciate it! 

Thanks for the help,

Chase

[Thomas Kühne]

Dear Chase, 

IMHO there are two ways to do that: 

(i) use THERMOSTAT/DEFINE_REGION to thermostat your surface. However, in that 

case you have to specify SUBSYS/VELOCITIES to assign the velocities of your 

molecule by hand or restarting them … 

(ii) Use MD/THERMAL_REGION/DEFINE_REGION, to define the surface AND your 

molecule, as well as their respective temeratures. However, this way you can only 

specify LAGEVIN for the surface and NVE for the molecule, which should be good enough. 

Cheers, 

Thomas

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==============================

Thomas D. Kühne

Dynamics of Condensed Matter

Chair of Theoretical Chemistry

University of Paderborn

Warburger Str. 100

D-33098 Paderborn

Germany

tdku...@mail.upb.de

+49/(0)5251/60-5726

[MD Simulation]

Thanks Thomas!

What setting would I use for MD/THERMOSTAT/REGION?  Would it still be GLOBAL or would it be MOLECULE?

On Monday, January 6, 2020 at 4:56:14 AM UTC-5, tkuehne wrote:

Dear Chase, 

IMHO there are two ways to do that: 

(i) use THERMOSTAT/DEFINE_REGION to thermostat your surface. However, in that 

case you have to specify SUBSYS/VELOCITIES to assign the velocities of your 

molecule by hand or restarting them … 

(ii) Use MD/THERMAL_REGION/DEFINE_REGION, to define the surface AND your 

molecule, as well as their respective temeratures. However, this way you can only 

specify LAGEVIN for the surface and NVE for the molecule, which should be good enough. 

Cheers, 

Thomas

Am 05.01.2020 um 16:50 schrieb MD Simulation <mdsimula...@gmail.com>:

Hi,

I need to run a simulation of a molecule being shot at a surface.  I'd like to do two things: 1) thermostat the surface and 2) assign a specific velocity to the small molecule.

I see in the MD/THERMOSTAT section, there is a keyword REGION...is this what I would want to do?

If anyone has some ideas, I would appreciate it! 

Thanks for the help,

Chase

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[Thomas Kühne]

Nope, this has nothing to do with that, it is to specifies to how many 

degrees of freedom the thermostat is coupled. If I recall it correctly 

GLOBAL means 3 DOF of the whole system and MASSIVE to all 

3N DOF. MOLECULE should be 3 per molecule, which for a QS 

calculations, where a molecule is identical to an atom shouldn’t be 

much different from MASSIVE. I personally don’t see any reason for 

GLOBAL anymore and always use MASSIVE and control if I would 

like to access dynamic or mere static equilibrium properties via the 

corresponding time constant. 

Cheers, 

Thomas

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[Nam Tran]

Dear Prof. Thomas and Chase,

I have a little confuse about the tag MD/THERMOSTAT/DEFINE_REGION. If some atoms are not listed in the region does it mean those atom are just simply follow the the Newtonian EOM?. In addition, what is the meaning of setting DEFINED in the tag MD/THERMOSTAT/REGION?

Regards

Nam