[gmx-users] electro-static interaction not made

abdullah ahmed abdullah_renk_ahmed at hotmail.com
Tue May 11 11:37:14 CEST 2010

Dear GROMACS users, 

I have a protein structure with two oppositely charged residues facing each other. They are close enough for an electrostatic interaction to occur between them. However, this does not occur. After minimization they are in the exact same positions as before. 

Is there some way to confirm that an electrostatic interaction is not 
being made in the structure with two charged residues facing each other?
 And if this is the case, do you have any idea as to why this is 

Perhaps the following information will prove helpful: 

I have another structure where there is only one charge (GLU) and one uncharged residue in the same positions as the charged residues in the previous structure. The coulomb energy values of the two structures after minimization do not show much difference (-3.9e+04 compared to -4.0e+4, where -4.0e+04 corresponds to the structure with two charges facing each other). Theoretically, this difference should be greater as the unsatisfied single charge is not as stable. To me the similar coloumb energies suggest that the electrostaic interactions are not being made in the structure with two opposite charges. 
My .mdp file is as follows:      ;
      ;    User spoel (236)
      ;    Wed Nov  3 17:12:44 1993
      ;    Input file
      cpp                 =  /usr/bin/cpp
      define              =  -DFLEXIBLE 
      constraints         =  none
      integrator          =  steep
      nsteps              =  1000
     ;    Energy minimizing stuff
     emtol               =  2000
     emstep              =  0.01

    nstcomm             =  1
    ns_type             =  grid
    rlist               =  1
    rcoulomb            =  1.0
    rvdw                =  1.0
    Tcoupl              =  no
    Pcoupl              =  no
    gen_vel             =  no

Thank you in advance!

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