GROMACS modification: No
I am trying to determine the Potential of mean force profile for a ligand passing through a membrane. I was planning to use gromac’s AWH tool. I would like to pull the ligand through the entire membrane (more than half the box). However, I keep getting error messages indicating that this is not permitted.
What mdp parameters do I have to use, if I want to pull the molecule through the membrane and across periodic boundaries?
The periodic boundary itself is irrelevant for all method in GROMACS.
What can be problematic is distances that larger than half the box size. I would think you can much a molecule up to half the box size above and below the membrane. Do you get an error when you attempt that?
With AWH you can have a periodic domain when the box size along the dimension you are pulling is fixed. But I think you do not want a periodic domain in your case.
Hi Hess, thanks for the prompt respons. This is very helpful. I pull the molecule along z and we used anisotropic coupling in umbrella simulations before. What mdp parameters should I use to pull along the full box hight?
Thanks a lot Sebastian
I assume that you use the membrane as a reference with cylinder pulling. In that case I would think you can pull to nearly half the box height both up and down from the center of the membrane. I must say that I have not tested this myself.