[gmx-users] overlaps atoms during solvation(genbox)

Vasumathi Velachi vas at fc.up.pt
Mon Aug 27 12:47:03 CEST 2012


I new in using Gromacs.

I used genbox to solvate my solute(gold+thiols), when I am doing so the 
resultant pdb have the overlaps between water molecule and gold. This 
overlaps is due to the missing information for gold in the file 
"vdwdradii.dat". In order to avoid the overlaps shall i increase vdwd 
radii while solvating or shall  I include the vdwd radii information for 
gold atoms in "vdwdradii.dat" file.

Thanking you in advance

Vasumathi Velachi

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