[gmx-users] The flat-bottomed position restrain in the topolgy file

[liuyong_1007 at dicp.ac.cn]

Dear gromacs usres,

The format of the flat-bottomed position restrain in the topolgy file is 
[position_restraints]
; num. atoms    func.type   g      r(nm)    k(KJ*mol-1*nm-2)   
    1              2        1       1.0         1.0
as given in the manual 5.0.2. 
But there is still another parameter not set. The reference position R_i ( see eq. 4.77 in the manal)is not given in the topolgy file.
How can this parameter be set ?

Thank you very much!
Yong Liu







liuyong_1007 at dicp.ac.cn