[gmx-users] Help simulating flow

[Ross Gunderson]

Hello gmx_users,

I am stuck on my simulation and not sure how to implement things in gromacs. Basically, I am looking to simulate flow of solvent over a lipid bilayer. I have a system (created by Charmm-GUI) of lipids and solvent (two separate group IDs in the gromacs) and I would like to apply a flow with the solvent.

- I would like to use acc-grps to move the solvent, but how do I verify this is working in my simulation? I do not see anything in the log file that indicates the acc-grps has been initiated. 

- I am trying to use nwalls=2, with pbc=xy, but this is currently an error, “DD cell 3 0 0 could only obtain 665 of the 667 atoms that are connected via constraints from the neighboring cells. This probably means your constraint lengths are too long compared to the domain decomposition cell size. Decrease the number of domain decomposition grid cells or lincs-order.”

- Lastly, I would like to define a dynamic group for a specific region of the solvent to apply the acceleration too. I realize this is probably impossible, but even if I can only accelerate the solvent above the lipid bilayer, that would be preferred.

Thank you for your time!
- Ross