[gmx-users] genbox output taking forever to complete

Justin A. Lemkul jalemkul at vt.edu
Sun Apr 17 21:28:47 CEST 2011

majid hasan wrote:
> Okay, so here is an output attached, for cubic box of length 10.
> Actually, the carbon atoms are all placed at   0<x<4,  0 <y< 2.5,   
> 0<z<3.5. While solvent and DNA atoms are in the region     4<x,y,z<6. So 

Then your box size is overkill.  All you're going to end up doing is adding tens 
of thousands of waters that do not serve any purpose for most applications. 
There is (in general) no need for a 4-nm buffer around your system.  Take your 
unsolvated coordinate file and run editconf -d 1 to obtain a more suitable box 
before trying genbox again.

> only DNA is solvated, while CNT is just lying outside. Though I might 
> have placed solvent in a cube of length 10 (using: editconf -f 
> spc216.pdb -o spc216.gro -box 10 10 10), could this be the reason?

Yes, as I said before - do not adjust the box of spc216.gro.  The genbox program 
takes the input solvent configuration (unmodified, please!) and tiles it across 
the box defined in the -cp configuration such that it fills the box.  If you 
make a solvent box with a bunch of empty space just to "fit" in your existing 
box, you accomplish nothing at all and genbox will probably chew up a lot of 
memory trying to make this exact fit.

> I am at the moment trying to solvate the whole system (in a cubic box of 
> 20) without specifying -box in editconf -o spc216.gro, but this is 
> taking long, its running for about half an hour  after reaching this 
> point: Reading solvent configuration "Quotation" Solvent configuration 
> contains 648 atoms in 216 residues. Is that much time normal, I am 
> running it on my laptop, which is 2GB Ram, and Dual Core ~1.4GHz processor?

That is an enormous box that will require a large amount of memory to 
accomplish.  Before trying to get a huge box to work, make sure you can do 
something more "normal" as I suggest above.  You haven't stated your overall 
purpose, but for only a very few particular tasks would you ever require a 
system this large for components as small as the ones you're dealing with.



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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