Dear lammps users,
I want to build a simulation of pulling a molecule away from a substrate for PMF computation.
I use fix smd command with mode “cvel” and keyword “tether”.
The command line as follows,
fix pull_up pull_up smd cvel 100 0.0001 tether NULL NULL 32.4273 0.0
The group “pull up” is at the position z = 21.87, and the surface of substrate is at z = 19.2.
I expect that the molecule will be pulled in +z direction because I set the velocity positive (+0.0001).
But it results in the opposite, with the molecule being pulled towards the substrate.
Furthermore, the molecule moved away from the substrate when I set cvel = -0.0001.
In the documentation, the definition of ‘R’ was not mentioned. I assumed it to be the distance between the “ghostatom” with distance R0 from xyz and the center of mass of the atom group. Is this correct?
In addition, the definition of the parameters xyz that follows the keyword “tether” is defined as one of the endpoints of the spring in the “Syntax” section. However, in the third paragraph of the “Definition” section, the spring is said to be connected to the “ghostatom” with distance R0 from xyz. These definitions seem to contradict. Is there anything wrong with the interpretation? If so, please explain the mechanism.
Thanks in advance.
Best regards,
XYB