Thank you so much!
> -----原始邮件----- > 发件人: "Jianguo Li" <ljg...@yahoo.com.sg> > 发送时间: 2012年10月31日 星期三 > 收件人: "Discussion list for GROMACS users" <gmx-users@gromacs.org> > 抄送: > 主题: Re: [gmx-users] steered pulling code on ligand-receptor complex > > 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 -- 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
