[gmx-users] solvation

Justin A. Lemkul jalemkul at vt.edu
Thu Aug 13 17:42:36 CEST 2009

Jamie Seyed wrote:
> Dear all,
> I want to know how can I use genbox to fill inside of the pore as well 
> as a layer outside. From the "man genbox" page I try to use -shell with 
> a negative value (?) but it put waters far from the outside of the pore 
> and I think it does not care about the sign. It seems strange to me 
> because when I had 10 10 10 in the last line of my f.gro, by a shell 0.5 
> or 0.2, I got a layer of few molecule around the pore, but when I change 
> it to 1. 1. 1., the water molecules generated far away. I appreciate if 
> someone tell me (1) how I can add water inside the pore and (2) why 

(1) The -vdwd option may help, or even -ci -nmol.  If you have a pore, wouldn't 
water diffuse in over time anyway during equilibration (assuming an otherwise 
correct setup and realistic physical model)?

(2) If you haven't re-positioned your system within the box, it probably doesn't 
make any sense.  The Gromacs convention is to place the corner of the box at the 
coordinate origin, and everything else is relative to that.  Is a 1-nm cubic box 
large enough to encompass your system?  If not, genbox is doing what it's told - 
filling a 1-nm box near the origin, and leaving everything else out.


> changing the box size will give a opposite result. Please advise..Thanks 
> in advance/Jamie
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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