GROMACS modification: No
I have read and run the free energy tutorial. I am not a molecular expert, but I would like to study some performance tests on GPU. So, my specific question is, how can I replace the current input with a larger one?
When I run the current input, Methane in water, only 200MB of GPU memory is used. Below, I would like to share my thoughts and see if I have understand the structure correctly.
1- In methane_water.gro, the number of atoms is 1793. If I want to use a larger input, I expect to have a .gro file with a larger number of atoms. Is there any repository for such .gro files?
2- Looking at the topology file, I see
[ molecules ] ; Compound #mols Methane 1 SOL 596
I would like to know if increasing the number of Methane or SOL alone is sufficient or there is a relation between these two parameters.
3- I know that based on the numbers in topol file, 1 and 596, atoms are defined in the coordinate file, .gro file. So, I was wondering how can I correctly enlarge the input.
Any feedback is appreciated.