|From:||Wes Barnett <w.barnett@...668...>|
|Date:||Mon, 28 Aug 2017 15:32:30 -0400|
On Mon, Aug 28, 2017 at 2:28 PM, Wes Barnett <w.barnett@...668...> wrote:On Mon, Aug 28, 2017 at 12:14 AM, Trung Nguyen <ndactrung@...24...> wrote:Hi Wes,it's possible to support triclinic boxes for fix rigid/npt and rigid/nph either by following the reference cited the fix rigid doc (Kamberaj et al), or by borrowing what is implemented in fix nh for updating the full box dimension tensor.However, please note that fix rigid/npt and rigid/nph with triclinic boxes would be mostly useful for the cases where you only have rigid bodies in the system. For systems of polymer-grafted rigid bodies like yours, I think the workaround along the line Axel suggested would work to the similar effect:# assuming you're having a triclinic box setupgroup nanoparticles type 1group tethers type 2fix 1 nanoparticles rigid/nvt temp ...fix 2 tethers npt temp 1.0 1.0 1.0 xy 1.0 1.0 10.0 ... dilate allfix_modify 2 press thermo_pressThe reason that it would work is that the simulation triclinic box is to be barostatted by the fix npt, which uses the system pressure tensor as feedback.Thanks Axel and Trung, this helps. I now see that this method is one of the options listed on the "fix rigid" page for using pressure coupling with a mixture of rigid and non-rigid molecules.Is the thermo_press compute modification (the last line) always necessary in a system like this?it is a case of "better safe than sorry". you can have only one fix changing the cell shape and volume, and that has to be coupled to the complete system pressure. that is usually for group all, i.e. what the thermo press keyword outputs. that should be done correctly by the npt or nph fix, but there is no harm in making it explicit.
fix 1 rigidGroup rigid/nvt molecule temp 1.0 1.0 0.5fix 2 nonRigidGroup npt temp 1.0 1.0 0.5 iso 5.0 5.0 5.0
fix 1 rigidGroup rigid/npt molecule temp 1.0 1.0 0.5 iso 5.0 5.0 5.0fix 2 nonRigidGroup npt temp 1.0 1.0 0.5 iso 5.0 5.0 5.0