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

Justin Lemkul jalemkul at vt.edu
Mon Aug 27 12:57:54 CEST 2012

On 8/27/12 6:47 AM, Vasumathi Velachi wrote:
> Hi
> 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.

The most straightforward solution is to add an entry for gold in vdwradii.dat. 
Make a local copy of the file in the working directory and make your modifications.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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