Dear All,
I am doing non-equilibrium MD simulation to analyze water transport properties through CNT. My model composed of a pool region filled by water molecules and CNT. I have applied an external force on water molecules inside the pool just in Z direction (pore axis). After simulation I expect that water molecules enter the pore from one end. But, via viz I see that water molecules enter both ends of the pore. Is it due to the periodic boundary condition?
Could anybody let me know why?
Thanks in advance
It would be easy to answer if I can see the .mpd and system coordinate file you used. I believe if you applied the pressure difference the water should be the uniderictional . The pbc may not be the reason because pbc only show such behaviour at the boundary but as I believe you have a bulk system and looking at end of CNT. So If you post your coordinate file like .pdb or .xyz and .mdp file the I can say.
Dear Hari,
Thank you very much for your kind reply. The attached is the LAMMPS data file includes the coordinates for CNT (C atoms are frozen) and water (Oxygen and Hydrogen atoms). Please kindly find the attached file
Thanks in advance
Hello Majid, after looking your system I guess your energy minimization is not sufficient, As I see lots of overlapings in your system. Once you can test again by further energy minization. But I might be wrong.
Dear Hari,
Could you please let me know that how can I minimize my model?
I have been trying to make an equilibration with constant pressure ( minimization ) over my model (A reservoir+CNT ) using NVE+langevin thermostat (as a script available in LAMMPS).
But it does not work (As mentioned at the script that it might do not work)
I would highly appreciated if help me
Thanks in advance
I have never used LAMMPS but I am sure there should be some script for NPT simulation. The at first step, Before using NVE+thermostating followed by NPT, Just geometry optimize/energy minimize the structure to reduce overlappings. Please consult the LAMMPS Manual.
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