[lammps-users] fix rigid

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1

Dear all,

I have 3 molecules( water , ether and copper) in my system.
can i use fix rigid for all as following:
fix 1 all rigid/nvt molecule temp 200 200 200

In other words, fix rigid\npt or rigid\nvt can be used for metals without restrictions?
Thanks
Farzane

2

fix rigid will do what the documentation says it does.
that is, when you use the “molecule” flag fix rigid will use the molecule id to define the rigid objects from all atoms in the fix group (i.e. all in this case).
from your (very vague) description, however, this doesn’t sound like it is what you may want.

please provide more details what kind of water potential you are using and what it is that you want to keep rigid and why then it would be easier to provide a more specific answer.

3

Thanks alot Axel.

I have one solution(water with an ether)…I want to use copper plate as a surface and set this solution on this surface…
for water tip4p has been used …I dont want divide my system to rigid and non rigid bodies.
is it possible?can i use fix rigid for all molecules and specially for copper plate?

I did this idea and used fix rigid/npt all… for my system.
my issue is : temperature result of the system is good, but the temperature of copper is not.

should i use fix_modify for this issue( temp of copper) or using this rigid command is not suitable for copper plate?

Thanks and regards
Farzane

4

there are multiple issues at hand:

  • there is no problem in defining groups and using different integrators. fix rigid is very inefficient on multiple small molecules, BTW.
  • I don’t see a need to use a variable cell integrator for the system you describe. why do you think you need it?
  • tip4p is usually handled in LAMMPS by using a tip4p coulomb pair style (with implicit point M) and then fix shake
  • there are well established protocols for modeling surfaces where you keep some atoms immobilized to represent the bulk and the remainder mobile. if you want to model a surface at a given temperature in contact with heat bath, then you need a more complex construct with a thermostatted region between the (unthermalized) surface layer and the (immobilized) bulk
  • for an “open” system you usually don’t want to employ a thermostat for the entire system unless you consider a semi-bulk surface and then you thermalize only the surface slab as described above after an initial global equilibration.

you still have not explained what object you specifically want to keep rigid. it also seems likely that you are confusing rigid bodies with immobilizing atoms.

axel.

5

Thanks for your reply.

I want to use rigid style for my ether molecule too, it is a cyclic ether (THF) and OPLS_ua force field has been used for it. There is no force for using rigid command for the copper plate. I fixed my copper plate with fix spring/self and it has no mobility.

at first, I also tried following commands as manual:

fix 1 solution rigid/npt…dilate all for rigid bodies(water and ether).

fix 2 copper nvt temp … for non rigid molecule i.e, copper.

fix 3 copper spring/self 10.

But the temperature of copper plate has fluctuation and is higher than target.

I can not find the result of this issue: why copper has temp fluctuation?

In my work. I want to rigid my molecules in the solution and the copper plate should be fix at certain temperature.
what command is better for it?

Thank you

6

Try replacing npt with nvt.

7

Ok, will do that.

Best regards
Farzane