[gmx-users] genbox output taking forever to complete
Justin A. Lemkul
jalemkul at vt.edu
Sun Apr 17 13:39:56 CEST 2011
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.
> *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.
> -- ========================================
> 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
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Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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