[gmx-users] genbox output taking forever to complete

majid hasan pu_majidhasan at yahoo.com
Sun Apr 17 21:27:10 CEST 2011 

Okay, so here is an output attached, for cubic box of length 10 (I removed some 
atoms to reduce the size below 50kB). 


Actually,  the carbon atoms are all placed at   0<x<4,  0 <y< 2.5,    0<z<3.5. 
While solvent and DNA atoms are in the region      4<x,y,z<6. So only DNA is 
solvated, while CNT is just lying  outside. Though I might have placed solvent 
in a cube of length 10  (using: editconf -f spc216.pdb -o spc216.gro -box 10 10 
10), could this  be the reason?

I am at the moment trying to solvate the whole  system (in a cubic box of 20) 
without specifying -box in editconf -o  spc216.gro, but this is taking long, its 
running for about half an hour   after reaching this point: Reading solvent  
configuration "Quotation" Solvent configuration contains 648 atoms in  216 
residues. Is that much time normal, I am running it on my laptop,  which is 2GB 
Ram, and Dual Core ~1.4GHz processor?

Thanks a lot,
Majid




________________________________
From: Justin A. Lemkul <jalemkul at vt.edu>
To: Gromacs Users' List <gmx-users at gromacs.org>
Sent: Sun, April 17, 2011 4:39:56 AM
Subject: Re: [gmx-users] genbox output taking forever to complete



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

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