Hi everyone, I'm trying to simulate the diffusion of a coarse-grained carbon nanoparticle (from Monticelli) into a coarse-grained DOPC lipid bilayer, to reproduce the results obtained by Wong-Ekkabut et al. I first assembled my bilayer in a box of size 7.5 x 7.5 x 7.5 nm3, and the results appeared legitimate. However, I'm now trying to repeat the experiment by placing the carbon nanoparticle at an initial position further away from the bilayer, and so I've resized my box to 15 nm x 7.5 nm x 7.5 nm.
In this case, what happens is that after solvation using genbox, if I carry out an energy minimization, the CNP drifts very close to the bilayer, rendering my increase of the box size redundant. To overcome this, I've tried restraining the positions of the CNP and the bilayer, but when I do this, my simulation 'blows up'. I'm not aware of how to overcome this problem. Would you be able to help me with this? Thanks! Regards Bharath K Srikanth -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
