[gmx-users] question about freezing a group

Linchen Gong glc02 at mails.tsinghua.edu.cn
Sat May 13 07:24:02 CEST 2006

Dear gromacs users,
    I'm doing a MD simulation of protein in water. I freeze an atom in z direction, e.g. freezdim N N Y, and afm pull another atom along -z direction, e.g. afm_dir = 0 0 -1 afm_rate1 = 0.01 afm_init1 equals the coordinate of the pulled atom. After about 200ps simulation, I found that the z coordinate of the pulled atom dropped with string, however the z coordinate of the frozen atom also dropped alot. I think z of the frozen atom should be constant, but why it drops?
    Waiting for your help.
    Thanks a lot!
                                                           Linchen Gong

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