doubt whit NPT-Gibbs ensemble
- vaninachiarpotti
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7 years 10 months ago #143
by vaninachiarpotti
Dear all,
I am relatively new Cassandra and will appreciate very much your opinion on the following question. I need to simulate the absorption of a liquid into a porous solid. In my model the solid is represented by a set of point particles (charges+ Lennard Jones) which are kept frozen in space. The liquid is made of rigid molecules that can translate and rotate. I thought the ensemble of choice for this type of simulation was NPT Gibbs Ensemble, i.e. one where the volume of the simulation cell containing the solid is forced to remain constant, by setting the size of the volume trial move to zero, and only liquid molecules can swapped between the two boxes.
Is my approach conceptually sound ?. Is Cassandra able to do this kind of simulation ?. I have been running some tests and in some cases I see liquid molecules appearing outside the simulation box of the crystal, this might have something to do with the coordinates of the solid are centered at the origin or not? Any help will be very much appreciated.
Best regards, and thanks for creating such a great simulation tool.
Vanina
I am relatively new Cassandra and will appreciate very much your opinion on the following question. I need to simulate the absorption of a liquid into a porous solid. In my model the solid is represented by a set of point particles (charges+ Lennard Jones) which are kept frozen in space. The liquid is made of rigid molecules that can translate and rotate. I thought the ensemble of choice for this type of simulation was NPT Gibbs Ensemble, i.e. one where the volume of the simulation cell containing the solid is forced to remain constant, by setting the size of the volume trial move to zero, and only liquid molecules can swapped between the two boxes.
Is my approach conceptually sound ?. Is Cassandra able to do this kind of simulation ?. I have been running some tests and in some cases I see liquid molecules appearing outside the simulation box of the crystal, this might have something to do with the coordinates of the solid are centered at the origin or not? Any help will be very much appreciated.
Best regards, and thanks for creating such a great simulation tool.
Vanina
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- ryangmullen
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7 years 10 months ago #146
by ryangmullen
Hi Vanina,
I think Cassandra will allow that setup, provided that both the liquid and solid boxes are cubic. It may not be very efficient since Cassandra will still attempt to change the volume of your solid box (by zero A^3) during half of the volume change moves.
As for molecules appearing outside the crystal, in Cassandra coordinates are only wrapped when a molecule gets moved. Since you aren't (or at least shouldn't be) moving, rotating, regrowing, or inserting the solid lattice, I don't think Cassandra will wrap the coordinates of any solid atoms back into the box. It will, however, correctly compute the energy using the minimum periodic image around each atom. If you are viewing your trajectory in vmd, you can wrap the coordinates of all atoms using the "pbc wrap" command, which is part of the PBCTools plugin.
Ryan
I think Cassandra will allow that setup, provided that both the liquid and solid boxes are cubic. It may not be very efficient since Cassandra will still attempt to change the volume of your solid box (by zero A^3) during half of the volume change moves.
As for molecules appearing outside the crystal, in Cassandra coordinates are only wrapped when a molecule gets moved. Since you aren't (or at least shouldn't be) moving, rotating, regrowing, or inserting the solid lattice, I don't think Cassandra will wrap the coordinates of any solid atoms back into the box. It will, however, correctly compute the energy using the minimum periodic image around each atom. If you are viewing your trajectory in vmd, you can wrap the coordinates of all atoms using the "pbc wrap" command, which is part of the PBCTools plugin.
Ryan
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