[gmx-users] changing particle vdw radius

jtomlins at purdue.edu jtomlins at purdue.edu
Mon Jun 16 18:35:13 CEST 2008

Dear Users,
I'm trying to do simulations of a particle of varying size in water with my own
potential.  I've grown a particle by modifying my LJ parameters over time; I
know that I can get a particle of 1nm radius and about 2300 TIP4P waters into a
box of 4.3x4.3x4.3 with a cutoff distance of 2nm.  I want to go to larger
particles and “growing” them is too time/computationally intensive.

I tried to use genbox to create the input with the larger volume particles in
two different ways unsucessfully. I am using version 3.3.3.

(1) I have tried to edit vdwradii.dat to change the radius as follows (I use Ar
for the name of my oil particle):
???  S      0.16 
???   Ar    1.0
GLY  MN1   0 
GLY  MN2   0 
However this doesn't seem to have any effect, no matter how large and outlandish
I make that number.

(2) I've also tired to specify vdw radius using the command line:
genbox -cp input.gro -cs tip4p.gro -p topol.top -vdwd 1.0
This seems to work up to about 0.5nm radius and the 4.3 cubic box.  If  I try to
go any larger then I get either a seg fault or the following error:
Program genbox, VERSION 3.3.3 
Source code file: ns.c, line: 1938 

Fatal error: 
One of the box vectors has become shorter than twice the cut-off length or
box_yy-|box_zy| or box_zz has become smaller than the cut-off. 
I know that if I enlarge the box it will work, but that requires a huge box. 
Where are the cutoff values that  genbox is using coming from?  I believe the
cutoff is what is giving me such problems as it is doing a cutoff of 3.27 for a
radius of 1.0nm.

Any hints as to what I'm doing wrong or missing?

Department of Chemistry
Purdue University
West Lafayette, IN 47907
(765) 494-5591
jtomlins at purdue.edu

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