I am trying to pull a subdomain of protein towards the center of the channel it makes. To do this I need to pull some aminoacids in -1, 0, 0 direction. I tried with this pull code
; Pull code pull = umbrella pull_geometry = direction_periodic pull_start = yes pull_nstfout = 1 pull_ngroups = 1 pull_group1 = nth pull_vec1 = -1.0 0.0 0.0 pull_rate1 = 0.001 pull_k1 = 2000 Without giving the reference pull_group0 I get a warning on the absolute system of reference, but I ignored it, because the same code worked when I tried to pull an ion in a fixed direction. However my group nth is pulled to the right and not to the left, as I was thinking it would do. I made two other trials, resumed here, because I am not sure of how exactly are the input used: TRIAL 2 pull_vec1 = 1.0 0.0 0.0 pull_rate1 = 0.001 TRIAL 3 pull_vec1 = 1.0 0.0 0.0 pull_rate1 = -0.001 But also those pulled my fragment towards right instead of left, that is outward of the channel. Then I tried to chose another part of the protein, that is on the opposite side, wondering if for some reason only positive pull are allowed, but now, the fragment is pulled to the left and not to the right, again outward. What can be the problem? Should I use a differente pull code (distance for example?). Is there anyway to make the pulling work using direction_periodic? -- View this message in context: http://gromacs.5086.n6.nabble.com/Pull-direction-is-always-outward-tp4947149.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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
