[gmx-users] Ion positioning

[Lieven Buts]

  I have been looking at a number of proteins, each
time following the following strategy:

    > pdb2gmx -f ...pdb... -o start.gro 
              -p start.top  -dummy hydrogens

    > editconf -f start.gro -d ...radius...
               -bt dodecahedron

    > genbox -cp out.gro -cs -o solv.gro
             -p start.top

    > grompp -v -f genion.mdp -o genion
             -c solv.gro -p start.top
    
    > genion -s genion.tpr -o ions.gro
             -g genion.log -pot pot.pdb
             -np ...number of Na atoms...

  In general this works well, but when I do this
for an RNAse T1 crystal structure with a net
charge of -9, adding 9 Na+ ions, some ions end up 
near the protein, but most end up in the
faces or on the edges of the water box. 
  The image at <http://ultr.vub.ac.be/~lieven/ions.png>
tries to illustrate the situation. Five of the nine
Na+ ions are near the protein, and four are forming
a square in one of the faces of the water box.


  This is the genion.mdp:

--------------------------------------
title               =  genion_hr
cpp                 =  /lib/cpp
;
constraints         =  all-bonds
integrator          =  md
dt                  =  0.002    ; ps !
nsteps              =  5000     ; total 10 ps.
nstcomm             =  1
nstxout             =  250
nstvout             =  1000
nstfout             =  0
nstlog              =  100
nstenergy           =  100
nstlist             =  10
ns_type             =  grid
rlist               =  1.0
;
coulombtype         =  pme
fourierspacing      =  0.1
pme_order           =  4
rcoulomb            =  1.0
rvdw                =  1.0
; Berendsen temperature coupling is on in two groups
Tcoupl              =  berendsen
tc-grps             =  Protein  SOL
tau_t               =  0.1      0.1
ref_t               =  300      300
; Energy monitoring
energygrps          =  Protein  SOL
; Isotropic pressure coupling is now on
Pcoupl              =  berendsen
Pcoupltype          = isotropic
tau_p               =  0.5
compressibility     =  4.5e-5
ref_p               =  1.0
; Generate velocites is off at 300 K.
gen_vel             =  no
gen_temp            =  300.0
gen_seed            =  173529
---------------------------------------------


  Any ideas what might be causing this behaviour?


-- 
Lieven Buts
Vrije Universiteit Brussel