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 listgmx-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 listgmx-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
Re: [gmx-users] genbox output taking forever to complete
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 0x4, 0 y 2.5,0z3.5. While solvent and DNA atoms are in the region 4x,y,z6. 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
Re: [gmx-users] genbox output taking forever to complete
majid hasan wrote: Okay, so here is an output attached, for cubic box of length 10. Actually, the carbon atoms are all placed at 0x4, 0 y 2.5, 0z3.5. While solvent and DNA atoms are in the region 4x,y,z6. So Then your box size is overkill. All you're going to end up doing is adding tens of thousands of waters that do not serve any purpose for most applications. There is (in general) no need for a 4-nm buffer around your system. Take your unsolvated coordinate file and run editconf -d 1 to obtain a more suitable box before trying genbox again. 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? Yes, as I said before - do not adjust the box of spc216.gro. The genbox program takes the input solvent configuration (unmodified, please!) and tiles it across the box defined in the -cp configuration such that it fills the box. If you make a solvent box with a bunch of empty space just to fit in your existing box, you accomplish nothing at all and genbox will probably chew up a lot of memory trying to make this exact fit. 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? That is an enormous box that will require a large amount of memory to accomplish. Before trying to get a huge box to work, make sure you can do something more normal as I suggest above. You haven't stated your overall purpose, but for only a very few particular tasks would you ever require a system this large for components as small as the ones you're dealing with. -Justin -- 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 listgmx-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
Re: [gmx-users] genbox output taking forever to complete
majid hasan wrote: Okay, so here is an output attached, for cubic box of length 10 (I removed some atoms to reduce the size below 50kB). Please do not attach coordinate files unless requested. Most people who are uninterested in this thread do not want to waste time downloading large emails that they don't need. It is substantially more efficient to post a link to an image in a freely accessible place, i.e. point #4: http://www.gromacs.org/Support/Mailing_Lists#Mailing_List_Etiquette Also, ad hoc removal of atoms is not helpful to solving your issue. -Justin -- 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 listgmx-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
Re: [gmx-users] genbox output taking forever to complete
Okay, thank you. Majid From: Justin A. Lemkul jalem...@vt.edu To: Gromacs Users' List gmx-users@gromacs.org Sent: Sun, April 17, 2011 12:28:47 PM Subject: Re: [gmx-users] genbox output taking forever to complete majid hasan wrote: Okay, so here is an output attached, for cubic box of length 10. Actually, the carbon atoms are all placed at 0x4, 0 y 2.5, 0z3.5. While solvent and DNA atoms are in the region 4x,y,z6. So Then your box size is overkill. All you're going to end up doing is adding tens of thousands of waters that do not serve any purpose for most applications. There is (in general) no need for a 4-nm buffer around your system. Take your unsolvated coordinate file and run editconf -d 1 to obtain a more suitable box before trying genbox again. 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? Yes, as I said before - do not adjust the box of spc216.gro. The genbox program takes the input solvent configuration (unmodified, please!) and tiles it across the box defined in the -cp configuration such that it fills the box. If you make a solvent box with a bunch of empty space just to fit in your existing box, you accomplish nothing at all and genbox will probably chew up a lot of memory trying to make this exact fit. 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? That is an enormous box that will require a large amount of memory to accomplish. Before trying to get a huge box to work, make sure you can do something more normal as I suggest above. You haven't stated your overall purpose, but for only a very few particular tasks would you ever require a system this large for components as small as the ones you're dealing with. -Justin -- 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 listgmx-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 -- gmx-users mailing listgmx-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
Re: [gmx-users] genbox output taking forever to complete
Alright, thanks. Majid From: Justin A. Lemkul jalem...@vt.edu To: Gromacs Users' List gmx-users@gromacs.org Sent: Sun, April 17, 2011 12:31:49 PM Subject: Re: [gmx-users] genbox output taking forever to complete majid hasan wrote: Okay, so here is an output attached, for cubic box of length 10 (I removed some atoms to reduce the size below 50kB). Please do not attach coordinate files unless requested. Most people who are uninterested in this thread do not want to waste time downloading large emails that they don't need. It is substantially more efficient to post a link to an image in a freely accessible place, i.e. point #4: http://www.gromacs.org/Support/Mailing_Lists#Mailing_List_Etiquette Also, ad hoc removal of atoms is not helpful to solving your issue. -Justin -- 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 listgmx-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 -- gmx-users mailing listgmx-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
[gmx-users] genbox output taking forever to complete
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? Thank You, Majid spc216.gro Description: Binary data -- gmx-users mailing listgmx-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
Re: [gmx-users] genbox output taking forever to complete
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. 2. Place DNA into box with CNT using genbox -ci -nmol 1 (or vice versa: CNT into DNA box, whichever order you want) 3. Solvate -Justin -- 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 listgmx-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
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 | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-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
Re: [gmx-users] genbox output taking forever to complete
Okay, thanks Justin!. 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 | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-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 -- gmx-users mailing listgmx-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
Re: [gmx-users] genbox output taking forever to complete
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? 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 | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-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 -- gmx-users mailing listgmx-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
