Hello, gmx users I've been doing SMD with gromacs program. being a new user, i have some questions. I want to pull a small oragnic compound throught a cyclic peptide nanotube which was inserted in the bilayer. 1. As some papers mentioned that the velocity is very important, what velocity should i use in the afm_rate1 option? i am also not sure about the afm_k1 option. 2. The nanotube is not parallel to any axis, what value should i use in the pulldim and afm_dir options? 3. should the reference group in my system be the nanotube and the group_1 be the small compound?
Thank you for you attention. Hope for your reply Huifang -- Huifang Liu (Ph.D. Student) School of Pharmacy Fudan University 138 Yi Xue Yuan Rd. Tel: (86-21)54237419 (O) Shanghai, China, 200032 Cell phone: +86-13764669357 E-mail: huifangliu1...@gmail.com Fax: (86-21)54237264
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