If you position restraint the receptor or only use several residues at the binding site, in both cases you limit your sampling to a small part of the phase space and the PMF may not be accurate, since the receptor may undergo conformational change upon ligand binding. Cheers --Jianguo
----- Original Message ----- From: 范聪 <fanc...@nenu.edu.cn> To: gmx-users@gromacs.org Cc: Sent: Tuesday, 30 October 2012, 20:04 Subject: [gmx-users] steered pulling code on ligand-receptor complex Hello, everyone! I'm a new user in gromacs, and now I have to perform a steered pulling code on a ligand-receptor complex. The ligand is to be pulled away from the binding site of the receptor, and umbrella sampling will be used to gain the PMF (potential mean force) curve. Then binding energy of the ligand-receptor complex would be estimated. The receptor contains 303 residues. While the ligand is pulling away, the whole receptor is restrained by posres, 1000 in x, y and z axis. Since the receptor is so large and umbrella sampling needs so much calculations, a very long time will be taken to complete the work. Now I have my question, is there anyway to reduce the taken time? Such as keeping only residues near the binding site to respect the whole receptor? Thank you all in advance! -- 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 -- 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
