[gmx-users] genbox output taking forever to complete
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
> 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
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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