Problem with rigid dynamics

Hi Everybody,

I am facing a problem with my rigid dynamics. My system contains a solute in a box of water. I need to rigid only the solute during the dynamics. But, for some reason, the solute molecule moves and all the water molecules are rigid. Here is the settings I used:

group water molecule <> 1 504
group solute molecule 505

velocity all create ${tempset} 4928459 rot yes dist gaussian

dump 1 all atom 400 dump_npt.lammpstrj
fix recentering solute recenter 0.0 0.0 0.0 units box
fix fxnpt solute rigid/npt molecule temp ${tempset} ${tempset} ${tempdamp} iso ${presset} ${presset} ${presdamp}
run 1000

Everything seems correct according to the output file:
group water molecule <> 1 504

1512 atoms in group water
group solute molecule 505
13 atoms in group solute

1 rigid bodies with 13 atoms

Any suggestions or help to solve this issue are greatly appreciated.

Many thanks.


You message sounds like you are confusing rigid with immobile. Which one is it that you want?

I just want to rigid the solute molecule while all the solvent molecules are flexible.

Sorry, I still get the impression that your command of the english language is insufficient to notice the difference.

This is not consistent with your input and it is rather difficult to judge since many important parts of your input are missing, so one has to guess what it does.

From your input I can tell the following:

  • it makes no sense at all to use fix rigid/npt for a single rigid object. temperature for a single object is ill defined.
  • the combination of fix rigid/npt and fix recenter will (in the trajectory) result in the only motion being any rotation of your solute (but the dynamics will still be computed as if there is translation). fix recenter doesn’t change the dynamics, it just changes the “visualization”. I generally prefer doing this after the simulation in the visualization software, if needed.
  • it is not at all clear how you infer from group definitions whether atoms are mobile or immobile. your input shows only time integration is applied to atoms in the solute group (and most of that is hidden by fix recenter).