<html><body><div style="color:#000; background-color:#fff; font-family:times new roman, new york, times, serif;font-size:12pt">Dear Gromacs Users, <br><br> 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: <br><br>pull = umbrella<br>pull_geometry = distance<br>pull_dim = N N
Y<br>pull_start = yes<br>pull_ngroups = 1<br>pull_group0 = DPPC<br>pull_group1 = DTC<br>pull_rate1 = 0.0<br>pull_k1 = 1000<br><br>Is the position restraints on DPPC molecules a solution to my problem?<br>Thanks in advance<br><br>Best regards <br><br><br>Giovani<br></div></body></html>