[gmx-users] genbox output taking forever to complete
majid hasan
pu_majidhasan at yahoo.com
Sun Apr 17 03:26:20 CEST 2011
Okay, thanks Justin!.
Majid
________________________________
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
>>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
-- ========================================
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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