[gmx-users] genbox output taking forever to complete

Justin A. Lemkul jalemkul at vt.edu
Sun Apr 17 03:19:39 CEST 2011

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.




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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