[gmx-users] genbox output taking forever to complete

majid hasan pu_majidhasan at yahoo.com
Sun Apr 17 06:07:44 CEST 2011

Okay, so I divided the procedure in three steps, and this does produce output 
immediately. But it seems that it doesn't put second molecule inside the box.
Here is the what I am doing:

1. editconf -f ssgcg.pdb -o ssgcg.gro -box 20 20 20  
2. genbox -cp ssgcg.gro -ci cntcapped.pdb -nmol 1 -o cntdna.gro
3. editconf -f spc216.pdb -o spc216.gro -box 20 20 20
4. genbox -cp cntdna.gro -cs spc216.gro -o solvated.gro
5. editconf -f solvated.gro -o solvated.pdb

I tried cubic boxes of different lenghts (10, 20, 100), but when I see the final 
file in solvated.pdb in rasmol, it seems that it puts dna, and cnt at a distance 
equal to the specified length of the box, and the water molecules are all 
clustered around dna only.

I also tried to create a box of lenght 100 20 20 and align dna along 1 0 0, but 
I still got the similar final output. 

My question is, what determines the distance between molecules inside the box, 
and how can I make sure that they are placed at a reasonable distance inside the 


From: Justin A. Lemkul <jalemkul at vt.edu>
To: Gromacs Users' List <gmx-users at gromacs.org>
Sent: Sat, April 16, 2011 6:19:39 PM
Subject: Re: [gmx-users] genbox output taking forever to complete

Justin A. Lemkul wrote:
> majid hasan wrote:
>> Dear All,
>> I am trying to add a single strand dna, and single walled carbon nanotube in a 
>>box using the genbox command. After typing following command:
>> genbox -cp cntcapped.pdb -cs spc216.gro -ci ssgcg.gro -nmol 1 -box 2 2 2 -o 
>> I get: Reading solute configuration
>> Containing 168 atoms in 1 residues
>> Initialising van der waals distances...
>> WARNING: masses and atomic (Van der Waals) radii will be determined
>>          based on residue and atom names. These numbers can deviate
>>          from the correct mass and radius of the atom type.
>> Reading solvent configuration
>> "Giving Russians Opium May Alter Current Situation"
>> solvent configuration contains 648 atoms in 216 residues
>> and then it takes forever to produce output.
>> I tried to generate an output with just one molecule in solvent (spc216.gro), 
>>and I ran into same problem. I suspect something is wrong with my solvent input 
>>(file attached). I copied this file from gromacs/tutor/water folder, though it 
>>looks reasonable when I view I view the corresponding .pdb file in rasmol (I 
>>created .gro file from .pdb file using editconf -f spc216.pdb -o spc216.gro).
>> Could anyone please guide me about possible issues, and how to resolve them?
> You're asking genbox to do far too many things at once.  Divide your procedure 
>into steps:
> 1. Set a box size using editconf for either the CNT or DNA.

I should say "a sensible box size" - a 2x2x2 box barely accommodates the 
smallest DNA fragment, and then certainly does not leave any room at all to 
accommodate the minimum image convention.



-- ========================================

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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