[gmx-users] genbox output taking forever to complete

[Justin A. Lemkul]

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 cntdna.gro,
>>
>> 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.

http://www.gromacs.org/Documentation/Terminology/Minimum_Image_Convention

-Justin

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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