So, I have started to learn NAMD because I need that for a project I will be doing in the next couple of months. I have some prior experience of MD with gromacs. I thought that since NAMD has a GUI frontend (VMD) it would be easier to learn but I am finding it much much harder to learn.
For my work, I need to simulate droplets of water (basically a fixed number of water molecules in vaccum, without any periodic boundary). However, I have no idea how or where to start. All of the tutorials online seems to focus primarily on proteins and how to simulate them so they are not of much help.
I tried to use the VMD solvate plugin to generate a box of solvent but there does not seem to be an option to control the actual number of water molecules (something similar to
gmx solvate -maxsol 200 from gromacs). It creates a box of water molecules, however, I don't know how to change the box to a sphere and remove the periodic boundary conditions (The water molecules does not need to be shifted because the MD run will automatically push it into a spherical shape).
Finally VMD solvate seems to take the topology for water from an internal file which gives TIP3P water, however, the psf file generated does not seem to have any parameters, so I am not sure how the simulation will run.
As for running the actual equilibriation, I am running into even more problems. QwikMD does not read the psf file, and I cannot figure out any way to change the boundary condition to spherical, or remove it.
So, my question is: How do I run simulations of water in NAMD ? (with the least amount of hassle)
A step-by-step answer would be the most helpful, but any answer is greatly appreciated.