Sorry forgot to write the subject in previous mail. Dear gmx-users,
We intend to perform free energy calculations by pulling a polypeptide along water-hexane interface. We need to pull the polypypeptide from the water layer towards the hexane layer (crossing the interface). For this we position restrained one hexane molecule in the bulk of hexane (pull_group0) and trying to pull the polypeptide (pull_group1) towards it. But though the polypeptide is getting pulled, the hexane layer is breaking in the process. The pulling options used are as follows, pull = umbrella pull_geometry = distance ; simple distance increase pull_dim = N Y N pull_start = yes ; define initial COM distance > 0 pull_ngroups = 1 pull_group0 = 3 pull_group1 = Protein pull_rate1 = 0.01 ; 0.01 nm per ps = 10 nm per ns pull_k1 = 1000 We have also played a bit with the pull rate and pull constant, but same thing happens. Are we doing something wrong? Can you please help? -- Prithvi Raj Pandey National Chemical Laboratory, Pune 411008. -- 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