I’m working on a workflow for simulating the deposition of water onto a surface to model the formation of amorphous solid water. The simulation uses a surface made of silica particles and water molecules comprising of four different atoms. The simulation works perfectly until the total number of atoms in the system hits 10,000, at which point due to the fixed formatting of the .gro files being used the columns indicating the type of atom and the number of atoms have no space between them, and hence the simulations stop working. Has anyone attempted to run a simulation of >10,000 particles before, and if so how did you get around the fixed formatting of the .gro file?
I’m well aware that simulations of this size are lengthy and require a lot of power, I don’t mind waiting for a long time to get results out of the simulations and I’m using a fairly beefy machine so computation lengths aren’t as long as they may seem!
A system of 10000 atoms is quite small for MD. The atom numbers in the gro, and pdb, files are irrelevant. The problem occurs at 100000 though, not 10000. Maybe you print a space when preparing the files? The gro file format is described in the manual. It’s fixed format with 5 digits for the atom number. Print the atom number % 100000 for systems with 100000 or more atoms.
I think part of the problem may be that the two hydrogens in the water are named HW1 and HW2, so I assume when the number of particles reaches 5 digits it touches these numbers and that causes an issue. I’ll change them to HWA and HWB to see if that makes a difference and pushes it up to 100,000.
Could you provide an example as to what you mean by the percentage? For example, if I had 110,000 particles, would I need to write 110%?