[gmx-users] some molecule clashing with another ?

Chih-Ying Lin chihying2008 at gmail.com
Wed Dec 30 23:37:29 CET 2009

My simulation broke down and the simulation procedues are as follows.

1. center a protein molecule in the simulation box
2. put 20 ligands around the protein with  " genbox " command
3. make sure that any atom of the ligands does not overlap on any atom of
the protein with Visulization-software.
4. solvent addition , with the command " genbox *-vdwd*  0.2   "
5. Addition of ions, with the command " genion "
6. Energy minimization of the solvated system
7. Position restrained MD

=> simulation broke down.
=> It is very probable that some molecule clashing with another.
=> since i have made sured that any atom of the ligands does not overlap on
any atom of the protein with Visulization-software,
      the clashed pair of the molecules are possible " solvent vs solvent
"    or     "solvent vs protein"       or       "solvent vs ligand "
=> however, from the Gromacs manual , command "genbox"
     " Solvent molecules are removed from the box where the distance between
any atom of the solute molecule(s) and any atom of the solvent molecule is
     than the sum of the VanderWaals radii of both atoms. A database (
vdwradii.dat <http://manual.gromacs.org/current/online/dat.html>) of
VanderWaals radii is read by the program, atoms not in the
     database are assigned a default distance -vdw."

=>  here is    vdwradii.dat  (the ligand is simply made of C, N, O, H)
; Very approximate VanderWaals radii
; only used for drawing atoms as balls or for calculating atomic overlap.
; longest matches are used
; '???' or '*' matches any residue name
; 'AAA' matches any protein residue name
???  C     0.15
???  F     0.12
???  H     0.04
???  N     0.110
???  O     0.105
???  S     0.16

My questions are
1. anything wrong of my simulation procedures ?
2. how to find the clashed molecules ?

Thank you
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