[gmx-users] No interaction between manually added atoms

Kamps, M. m.kamps at student.rug.nl
Tue Nov 15 13:44:52 CET 2016

Dear GMX-users,

I'm experiencing difficulty with my manually added atoms to create a
metallic surface within GROMACS. My goal is to create a surface (at this
point metallic, Al) and let it interact with a protein.
In my current situation I've only modelled the aluminium surface
(non-bonded surface). The EM drops to a minimum in only 8 steps (first red
flag?), the NVT and NPT equilibrium look ok, but during the MD run the
surface disassembles like it is made up of loose sand. There is no
interaction at all between my individual atoms. What did I do wrong? Or
what did I forget to do?

I created the surface by defining one single Aluminium atom in a pdb file,
which i converted via pdb2gmx. To enable this, I added a Al.rtp file to a
CHARMM27 forcefield, this file contains these lines:

[ bondedtypes ]
; bonds  angles  dihedrals  impropers
     1       1          1          1
[ AL ]
 [ atoms ]
; name  type  charge  chargegroup
    AL    AL   0.000     0

Furthermore, to the atomtypes.atp file I added this line:

AL    26.981539 ;    Aluminium mass

To the ffnonbonded.itp file I added this line:

AL    13    26.981539    0.000    A    0.2617500000    0.300000

Where the last two numbers relate to the Lennard-Jones potential. Although
these values are not based on any scientific literature (at this point),
they should show some interaction?

When I put the atom into pdb2gmx this is my output Al.gro file:

    1AL      AL    1   0.000   0.000   0.000
   0.00000   0.00000   0.00000

This atom is then replicated with insert-molecules to form an FCC crystal,
using an xyz coordinate file. The result is a nicely stacked (small slab
of) surface consisting of 256 atoms. The topology file looks like this:

[ moleculetype ]
; Name            nrexcl
AL               3

[ atoms ]
;   nr       type  resnr residue  atom   cgnr     charge       mass
typeB    chargeB      massB
; residue   1 AL  rtp AL   q  0.0
     1         AL      1     AL     AL      1          0    26.9815   ;
qtot 0

Including the usual lines such as include water models, ion models etc..
The surface is then put in a box (with 1.5 nm distance to edges, in all
directions) and solvated with tip3p water molecules. Can someone help me?


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