Dear Gromacs Users, I am trying to extract the potential of mean force of a small molecule in a DPPC bilayer. To this end, I applied the methodology described in an online manual written by Justin Lemkul. My problem is when I run biasing simulations of the molecule near the interface (DPPC/water), some lipid molecules move to the water phase. This has as a consequence a local disorder of the bilayer. Below is the parameters I employ for the pull code:
pull = umbrella pull_geometry = distance pull_dim = N N Y pull_start = yes pull_ngroups = 1 pull_group0 = DPPC pull_group1 = DTC pull_rate1 = 0.0 pull_k1 = 1000 Is the position restraints on DPPC molecules a solution to my problem? Thanks in advance Best regards Giovani
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