[gmx-users] Problems with SMD using gromacs

huifang liu huifangliu1985 at gmail.com
Thu Mar 5 09:12:52 CET 2009

Hello, gmx users
I've been doing SMD with gromacs program. being a new user, i have some
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 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: huifangliu1985 at gmail.com Fax: (86-21)54237264
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