thermodynamics integration from scratch using cp2k

  1. 2 ions in 512 water system is using to calculation the Potential of Mean Force (PMF) for ion pair. ( I was using 64 water system where the size of the box is only about 12.0Å, the PMF can only exceed to 6.0Å, if I use 512 water system the box size can be more than 24Å the PMF can exceed to 10.0Å. )

  2. I need to know the size of the box with such number of water and ion in the system. (maybe not necessary for such big system, I put it here for smaller system and large concentration ionic solutions) Details are in my code.

    cal_density.py

    cal_density_512h2o.py

    The box size calculated for NaCl in 512H2O is 24.8736639347 Å.

  3. Generate the initial structure for my simulation. I use gromacs and vmd to do that. First using genbox tool in gromacs to generate a box of water with 514 water in it. The size is a little bit larger to make sure enough water molecules can be included.

    genbox_d -cs spc216.gro -box 2.52 2.52 2.52 -maxsol 514

    In this way, I got a out.gro file. I will rename it to h2o514.gro file. And edit it to change the last two water to a Na ion and a Cl ion. Also the size of the box will be changed as well as the index of the atoms and the total number of atoms in the top of the file. Then I rename it to h2o512NaCl.gro. I have the final version of it here. h2o512NaCl.gro

    I would like to use psf and xyz file for the input of topology information and coordinations in to cp2k. VMD is used here for this task. So I use the script I wrote for vmd. tr_psf512.vmd it used in this way.

    vmd -e tr_psf512.vmd

    The files I got here is H2O512NaCl.xyz, and H2O512NaCl_gro.psf . They also need to be edited (OW -> O, HW1, HW2 -> H, the atom mass, and change the form of psf to upsf which can be loaded by cp2k). The final version of these two files are given here. H2O512NaCl.xyz H2O512NaCl_gro.psf (This structure is not good enough for directly calculation since the cell size is not the same. I will try to use packmol to regenerate another initial structure for the calculation later.)

  4. The force field I am using is SPCE/HMN. An online energy unit convertion tool is used for the parameters.

  5. The input file for cp2k. It is the input file for constraint dynamics. The lagrange multiplier will print out for the constraint force for the thermodynamics integration calculation.