[gmx-users] pulling direction of molecule through a cyclic peptide nanotube

Alireza Mansouri alireza_mansouri89 at yahoo.com
Wed Apr 13 20:53:48 CEST 2016

Dear gromacs userI have been doing umbrella sampling with gromacs 5.1.2 and I want to pull a small molecule through a cyclic peptide nanotube. When it ran, the molecule didn't go through the tube instead it began to fluctuate around the wall of tube.My pull code looks like this:; Pull codepull                    = yespull_ngroups            = 2pull_ncoords            = 1pull_group1_name        = PNTpull_group2_name        = LIGpull_coord1_type        = umbrella    pull_coord1_geometry    = distance pull_coord1_vec         = 0 0 1pull_coord1_groups      = 1 2pull_coord1_dim         = N N Ypull_coord1_rate        = 0.01         pull_coord1_k           = 1000         pull_coord1_start       = no          Can I solve this problem?Thank you for your attention. Hope for your replyMansouri

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