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 <jalem...@vt.edu> To: Gromacs Users' List <gmx-users@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 <jalem...@vt.edu> > *To:* Gromacs Users' List <gmx-users@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 > > ======================================== > -- gmx-users mailing list gmx-users@gromacs.org ><mailto:gmx-users@gromacs.org> > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at >http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or >send it to gmx-users-requ...@gromacs.org ><mailto:gmx-users-requ...@gromacs.org>. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- ======================================== 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 ======================================== -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
solvated_att.gro
Description: Binary data
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