Water diffusion in MOFs (verbosity level of output file)

Dear all,

I was wondering if anyone could kindly help me with the following two questions. Please let me initially explain the simulation system:

I am trying to simulate diffusion of TIP4P water molecules in MIL125 MOF. The initial configurations of water molecules are obtained from a previously run GCMC simulation. At this stage, I am just trying to perform a short NVE run to make sure that all my input and force field parameters are read correctly by LAMMPS and there is no inconsistency. The attached input file runs without any apparent problem, however I still have the following questions/doubts:

1- Is there any way to output all the force field parameters that are actually “read” by LAMMPS for every pairwise interaction at the beginning of a simulation run? This would be very helpful to ensure the intended force field parameters are defined correctly by the user. Normally, this can be achieved by increasing verbosity level of output files in a simulation package. However, I couldn’t find out whether LAMMPS supports a similar feature.

2- In the attached input file, I have defined cross Lennard-Jones potentials explicitly. They are defined between Oxygen and Hydrogen atoms of TIP4P water molecules with 6 other atom types belonging to the adsorbent framework (i.e. MOF). At this stage, I am unsure whether I need to define a similar set of pairwise interactions for coulombic potentials (something similar to lines 68 and 69 of the input file which are currently commented out) or the kspace_style takes care of all the cross coulombic interactions between water and framework atoms?

Any advice will be very much appreciated.

Best regards,

Amir

in.lammps (4.64 KB)

Dear all,

I was wondering if anyone could kindly help me with the following two questions. Please let me initially explain the simulation system:

I am trying to simulate diffusion of TIP4P water molecules in MIL125 MOF. The initial configurations of water molecules are obtained from a previously run GCMC simulation. At this stage, I am just trying to perform a short NVE run to make sure that all my input and force field parameters are read correctly by LAMMPS and there is no inconsistency. The attached input file runs without any apparent problem, however I still have the following questions/doubts:

1- Is there any way to output all the force field parameters that are actually “read” by LAMMPS for every pairwise interaction at the beginning of a simulation run? This would be very helpful to ensure the intended force field parameters are defined correctly by the user. Normally, this can be achieved by increasing verbosity level of output files in a simulation package. However, I couldn’t find out whether LAMMPS supports a similar feature.

you can use the “write_coeff” command.

2- In the attached input file, I have defined cross Lennard-Jones potentials explicitly. They are defined between Oxygen and Hydrogen atoms of TIP4P water molecules with 6 other atom types belonging to the adsorbent framework (i.e. MOF). At this stage, I am unsure whether I need to define a similar set of pairwise interactions for coulombic potentials (something similar to lines 68 and 69 of the input file which are currently commented out) or the kspace_style takes care of all the cross coulombic interactions between water and framework atoms?

pair style lj/cut/tip4p/long already contains coulomb interactions (with special treatment of the location of the point M for TIP4P water molecules, which is computed on the fly while the Oxygen atom is skipped as it has no charge). this is the short range part. the long range part is computed in pppm/tip4p

axel.