Dear members,
I want to understand the working mechanism of the Langevin fix. Actually, I want that polymer in a box to do Langevin dynamics in an implicit solvent, so I use two fixes which give me the NVT ensemble.
fix fxnve all nve
fix fxlange all langevin 300 300 10000 86975
These two combine and give me the NVT ensemble if I want to understand how it is happening. How can I know?
Second, I am running the oscillatory method to deform a triclinic box, using the deform syntax,
variable gamma equal 0.1
variable A equal Ly*${gamma}
variable Tp equal 500000
fix wig all deform 1 xy wiggle A Tp units box flip no
When I visualise the trajectory in OVITO, I can see that one bottom surface is fixed and the top surface is deforming with some amplitude. The PBC condition is periodic, so I want to understand how it works when deformation occurs.
Is it only working on the Box, or is it working on the polymer chain and the box together?
Thank you.
No they don’t. Fix nve plus fix langevin will give you are system with a controlled temperature, but the Langevin dynamics is different from an NVT ensemble in the same way that fix nve plus fix temp/berendsen or fix temp/rescaled or most other thermostats will not give you NVT (with the exception of fix csvr, IIRC). The NVT statistical mechanical ensemble has a very strict definition and only something like the fix nvt integrator is compatible (provided you don’t use its drag option).
Pick up a text book about statistical mechanics or statistical thermodynamics and learn from it. Also you should read the LAMMPS documentation describing the functionality and any references it points to.
The statements about the NVT ensemble imply that there are no other system manipulation. Using fix deform is violating that. So even if you would be using fix nvt, you would no longer be running an equilibrium simulation by adding fix deform. The action of fix deform will continuously add energy to the system and the thermostat algorithm has to remove it for keeping the temperature.
How fix deform operates (and how it can be changed) is explained in its documentation in the LAMMPS manual. If you have questions beyond that, you have to ask more specific questions.
It can do either, what happens depends on the settings. Again, please study the documentation of the command. That is what it is for and why developers write documentation.