GROMACS version: 2021.2
GROMACS modification: No
Hello everyone,
I’m new to the forum and was wondering if anyone has experienced the coarse-grained beads in their models overlapping with each other. To provide some context, I am trying to simulate a polymer system using a MARTINI force field. When I increase the number of polymer chains in my models, the CG beads seem to overlap more, inflating the free volume a lot more than density would have predicted.
Here is a quick depiction of what I think is happening:
The images below the drawing are a section of an isosurface slice from the two systems with seemingly different degrees of bead overlap. The left slice is a 6 polymer chain system that appears to have less bead overlap while the right slice is a 14 polymer chain system that appears to have more bead overlap.
Are there others who have observed this issue in their models? If so, are there any suggestions or solutions regarding the potential cause of the problem (or if it is a problem at all)? I’m a bit puzzled and would love any suggestions.
It’s also worth noting that I’m not too confident in my equilibration methods and am still trying to improve/adjust the simulated annealing methods for systems with different numbers of polymer chains.
Thanks again for you time and would love any help!