[gmx-users] genbox output taking forever to complete

[Justin A. Lemkul]

majid hasan wrote:
> 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 solvent?
> 

I'm not entirely clear on what you're seeing, but you need to omit step 3 above. 
  Defining a huge box for a small cube of solvent will lead to incorrect 
solvation.  genbox will read a solvent configuration and create identical blocks 
until the unit cell is full.  Defining a larger box in which you place the 
solvent prevents this from working.

Positions of molecules inserted with genbox -ci -nmol are random.  If you want 
to define a specific orientation or position in the box, use editconf 
-center/-translate/-rotate as necessary.

-Justin

> Thanks,
> 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 <http://vt.edu> | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/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

========================================