<html><body><div style="color:#000; background-color:#fff; font-family:times new roman, new york, times, serif;font-size:12pt"><div>Dear Gromacs Users,</div><div><br></div><div>I am trying to study the free energy of binding in a protein-ligand complex. <br></div><div>I use the following pull input in my mdp file:</div><div>; Pull code<br>pull = umbrella<br>pull_geometry = distance <br>pull_dim = N Y N<br>pull_start = yes <br>pull_ngroups = 1<br>pull_group0 = Protein<br>pull_group1 = GLC<br>pull_rate1 = 0.005 <br>pull_k1 =
1000 <br></div><div><br></div><div> if I am pulling in 'Y' direction, is it necessary to make sure that the distance between the COM (of the protein and ligand) = distance between the Y coordinates, i.eY(pro)-Y(lig), ?<br></div><div>---- VMD commands ----<br></div><div>set pro [atomselect top "protein"]<br><br>set glc [atomselect top "resname GLC"]</div><div><br></div><div>set A [measure center $pro weight mass]<br>40.33518600463867 35.01163101196289 38.7291374206543</div><div><br>set B [measure center $glc weight mass]<br>40.591331481933594 39.440189361572266 38.494876861572266</div><div><br clear="all">vecdist $A $B<br>4.4421411021009884</div><div><br>Y(pro)-Y(lig) = 4.42855835</div><div><br></div><div>Best,</div><div>nahren<br></div></div></body></html>