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Hi.<div><br></div><div>I am trying to the the PMF of transferring a drug molecule from the aqueous phase to a lipid bilayer.</div><div><br></div><div>In order to minimize the effects of membrane undulations I tried to use pull_geometry=cylinder.</div><div><br></div><div>Whenever I run a short simulation with umbrella sampling starting from a configuration with the drug molecule way above the bilayer</div><div>the drug molecule is pulled into the bilayer rather rapidly. It appears as if the distance between the cylinder's COM and </div><div>the drug molecule's COM is supposed to be zero since it is pulled to the center of the membrane. </div><div><br></div><div>Since I apply an umbrella potential I find this weird and I would of course like the molecule to</div><div>"stay put" at that current z-position. Probably I set up the pull code wrong. Here are my options:</div><div><br></div><div><div>pull = umbrella</div><div>pull_geometry = cylinder</div><div>pull_dim = N N Y</div><div>pull_ngroups <span class="ecxApple-tab-span" style="white-space:pre">        </span> = 1</div><div>pull_rate1 <span class="ecxApple-tab-span" style="white-space:pre">        </span> = 0.0</div><div>pull_k1 <span class="ecxApple-tab-span" style="white-space:pre">        </span> = 1000</div><div>pull_start = yes</div><div>pull_init1 = 0.0</div><div>pull_vec1 = 0.0 0.0 1.0</div><div>pull_pbcatom0 = 0</div><div>pull_ngroups = 1</div><div>pull_group0 = DPPC</div><div>pull_group1 = drug</div></div><div><br></div><div>Have not decided the radii of the cylinder yet, but that is besides the point here.</div><div><br></div><div>I run with the 4.5.5 version and cannot figure what the problem is.</div>                                            </div></body>
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