Re: [gmx-users] Genbox center of box
On 6/10/13 12:13 PM, Matt Bawn wrote: I am beginning a simulation of my system following the lysozyme tutorial but when I try to use genbox to solvate my system it asks me to provide the coordinates of the center of the box. I have previously been successfully able to enter the same commands without this prompt appearing from gromacs. Can anyone let me know what I'm doing wrong please? Can you please provide your exact sequence of commands (up to, and including, genbox) and the exact error message (copied and pasted from the terminal)? Which version of Gromacs are you using? -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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 box size problem
genbox works best when the box size of the solute is defined as the same as of the water one used to solvate it. So you can build a water box with the dimensions you want and them use it. You can build a water box by using genconf -nbox and use a script to cut to the dimensions you need, minimize, equilibrate ... Using a bigger box size should work too but it might need to be positioned/centered correctly and the solute too ... On Apr 29, 2013, at 11:30, Alexander Björling alex.bjorl...@gmail.com wrote: Dear users, I am trying to solvate a MARTINI model, using a pre-equilibrated coarse-grained water box. This usually works fine with the following command. genbox -cs water-1bar-303K.gro -cp 01min.gro -o 02solv -vdwd 0.21 When I recently increased the box size things started going wrong. As the simulation box got bigger than the (-cs) water box, the solvated structure ended up containing clear block-shaped regions of higher and lower solvent density. I obviously tried stacking the (-cs) box first to make it bigger than the box in the (-cp) file, genconf -f water-1bar-303K.gro -o water-1bar-303K_big.gro -nbox 3 3 3 but the problem persisted. Waters actually coincide in the solvated structure, so energy minimization is obviously hopeless. Is genbox behaving unexpectedly or is this likely an input problem? Cheers, Alex -- 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 box size problem
On 4/29/13 5:30 AM, Alexander Björling wrote: Dear users, I am trying to solvate a MARTINI model, using a pre-equilibrated coarse-grained water box. This usually works fine with the following command. genbox -cs water-1bar-303K.gro -cp 01min.gro -o 02solv -vdwd 0.21 When I recently increased the box size things started going wrong. As the simulation box got bigger than the (-cs) water box, the solvated structure ended up containing clear block-shaped regions of higher and lower solvent density. I obviously tried stacking the (-cs) box first to make it bigger than the box in the (-cp) file, genconf -f water-1bar-303K.gro -o water-1bar-303K_big.gro -nbox 3 3 3 but the problem persisted. Waters actually coincide in the solvated structure, so energy minimization is obviously hopeless. Is genbox behaving unexpectedly or is this likely an input problem? I have seen this exact problem posted before. The coordinates of the water box provided by MARTINI have some coordinate values that basically coincide across the periodic box. With genconf, you can apply the -dist option to space them out slightly, then re-equilibrate before using the new configuration as input into genbox. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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 error
On 1/13/13 11:00 AM, Kieu Thu Nguyen wrote: Dear All, When i use the command genbox -ci single.gro -nmol 175 -box 7.5 7.5 7.5 -try 100 -o 175_noW.gro the error is Segmentation fault (core dumped) What does it mean ? Google can tell you all about segmentation faults. You probably ran out of memory. genbox is a memory hog, and when you're trying to insert lots of molecules into a box, it gets progressively harder to find space for them. The best solution is to either: 1. Use a larger box and equilibrate to achieve the desired size 2. Insert fewer molecules at a time -Justin And if i reduce the -try value, the out put file does not contain the right number of residues (not 175, and less than). Thank for any help ! Regards, KT -- Justin A. Lemkul, Ph.D. Research Scientist 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 did not run?
On 1/2/13 4:20 AM, Mijiddorj wrote: I am a new user of Gromacs, I have problem with genbox. When I run genbox following error occurred:Program genbox, VERSION 4.5.5Source code file: /build/buildd/gromacs-4.5.5/src/gmxlib/futil.c, line: 491File input/output error:/home/mijiddorj/Desktop/Tutorial02/1AKI1.topFor more information and tips for troubleshooting, please check the GROMACSwebsite at http://www.gromacs.org/Documentation/ErrorsHow can I fix this problem?Mijiddorj The specified file does not exist in the working directory. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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 -nmol, atoms removed
On 12/31/12 9:41 PM, Xu Dong Huang wrote: Dear Advanced Gromacs users, I'm trying to generate a solvated system with 1 solute (In my case 3). I do genbox -cp polymer.gro -nmol 2 -ci polymer.gro -cs water.gro -o polymer_solv.gro -p polymer.top My polymer molecule contains 201 atoms. box size 45x45x45 and it generates a system with the following messages: Found 1 molecule type: W ( 1 atoms): 4259200 residues Calculating Overlap... box_margin = 0.315 Removed 0 atoms that were outside the box Neighborsearching with a cut-off of 0.315 Table routines are used for coulomb: FALSE Table routines are used for vdw: FALSE Cut-off's: NS: 0.315 Coulomb: 0.315 LJ: 0.315 System total charge: 0.000 Grid: 254 x 254 x 254 cells Successfully made neighbourlist nri = 1851, nrj = 1983 Checking Protein-Solvent overlap: tested 867 pairs, removed 277 atoms. Checking Solvent-Solvent overlap: tested 1100 pairs, removed 0 atoms. Added 4258923 molecules Generated solvent containing 4258923 atoms in 4258923 residues Writing generated configuration to star_solv.gro star polymer Output configuration contains 4259727 atoms in 4258971 residues Volume : 512000 (nm^3) Density: 2539.37 (g/l) Number of SOL molecules: 0 **My problem is, the output configuration contains unequal amount of atoms and residues, and when I do the subtraction, the difference is the exact amount of atom of my original polymer molecule. (I'm assuming genbox removed my molecule out of the box) -How can I prevent that from happening? So that I can put as many additional polymer in the solvated system as I want? You're doing too much at once. Run the -ci -nmol options in one step, then solvate with -cs. You can also specify exact starting positions for each individual molecule with editconf -center, which may be a more foolproof solution for complex systems. As I recall, -ci has issues with multi-residue molecules, but perhaps that's an old issue and is no longer relevant. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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 -nmol, atoms removed
Thank you very much. I got it sorted out by following your advice. Xu Dong Huang Chemical Biochemical Engineering Rutgers School of Engineering xudo...@eden.rutgers.edu On Dec 31, 2012, at 10:23 PM, Justin Lemkul jalem...@vt.edu wrote: On 12/31/12 9:41 PM, Xu Dong Huang wrote: Dear Advanced Gromacs users, I'm trying to generate a solvated system with 1 solute (In my case 3). I do genbox -cp polymer.gro -nmol 2 -ci polymer.gro -cs water.gro -o polymer_solv.gro -p polymer.top My polymer molecule contains 201 atoms. box size 45x45x45 and it generates a system with the following messages: Found 1 molecule type: W ( 1 atoms): 4259200 residues Calculating Overlap... box_margin = 0.315 Removed 0 atoms that were outside the box Neighborsearching with a cut-off of 0.315 Table routines are used for coulomb: FALSE Table routines are used for vdw: FALSE Cut-off's: NS: 0.315 Coulomb: 0.315 LJ: 0.315 System total charge: 0.000 Grid: 254 x 254 x 254 cells Successfully made neighbourlist nri = 1851, nrj = 1983 Checking Protein-Solvent overlap: tested 867 pairs, removed 277 atoms. Checking Solvent-Solvent overlap: tested 1100 pairs, removed 0 atoms. Added 4258923 molecules Generated solvent containing 4258923 atoms in 4258923 residues Writing generated configuration to star_solv.gro star polymer Output configuration contains 4259727 atoms in 4258971 residues Volume : 512000 (nm^3) Density: 2539.37 (g/l) Number of SOL molecules: 0 **My problem is, the output configuration contains unequal amount of atoms and residues, and when I do the subtraction, the difference is the exact amount of atom of my original polymer molecule. (I'm assuming genbox removed my molecule out of the box) -How can I prevent that from happening? So that I can put as many additional polymer in the solvated system as I want? You're doing too much at once. Run the -ci -nmol options in one step, then solvate with -cs. You can also specify exact starting positions for each individual molecule with editconf -center, which may be a more foolproof solution for complex systems. As I recall, -ci has issues with multi-residue molecules, but perhaps that's an old issue and is no longer relevant. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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 Not enough memory
Thanks..You are right...The last line of gro file says 250 so it is in nm!... On 10 October 2012 12:30, Christopher Neale chris.ne...@mail.utoronto.ca wrote: Sounds like you ran out of memory. Many clusters have a few large-memory nodes. Can you use one of those? It's failing on a call for 1.3 Gb of memory, which by itself isn't really a lot... Also, can you confirm 250 A box length, not 250 nm box length? Gromacs defines length in units of nm. Chris. -- original message -- I am trying to build a polymer in solvent system by solvating my fully extended polymer chains in a box of size 250 250 250 A. I am adding 4500 solvent molecules as below genbox -cp Solute.gro -ci solvent.gro -o solvated.gro -nmol 4500 Adding solvents is a slow process and takes much time and at the end I get: Program genbox, VERSION 4.5.4 Source code file: smalloc.c, line: 214 Fatal error: Not enough memory. Failed to realloc 1338273212 bytes for grid-nra, grid-nra=0x0 (called from file nsgrid.c, line 483) For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Is this happening because of the huge amount of free space to be filled with the solvent? Please help me. -- Thanks, -- 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 -- Thanks, J. N. -- 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
Gavin Melaugh wrote: Hi all I have a system of 40 solute molecules in a solvent of 480 crown ether molecules. I am not trying to insert 100 methane molecules into this relaxed and well equilibrated structure using genbox. There are clearly visible cavities in the fluid but genbox only alllows the insertion of 8 methane molecules. How can I circumvent this problem ? The command I use is genbox -cp test.gro -ci methane.gro -nmol 100 -try 5 -p combined.top where combined.top includes all three itp files, and test.gro is the initial solute and solvent configuration. You might try reducing the value used for -vdwd in genbox, or otherwise shrinking the vdW radii in vdwradii.dat, but be warned that if you have to finesse the system too much, likely any resulting simulation will be extremely temperamental, if you can even get it to run. -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,genconf
saly jackson wrote: Hi all Would you please let m eknow f we use 'genconf' after that we must use 'genbox' before applying 'grompp'? It depends entirely upon what you want to do. I could think of a dozen ways to combine both tools, in different orders, to achieve completely different tasks. If you want a specific answer to solve a specific task, ask a specific question. -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
On 16/01/12, vidhya sankar scvsankar_...@yahoo.com wrote: Hello Justin, Thanks for your patient reply I would like to solvate my molecules with specific number of water molecules what option is a suitable to do that ? in editconf with regards S.Vidhya sankar See genbox -h. There is an option to set an upper bound on the number of solvent molecules added. It's up to you to choose a suitable volume beforehand. Mark -- 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
You can use the command genbox -cs with the option -maxsol number to specify the number of water molecules Good luck Cuong 2012/1/16 vidhya sankar scvsankar_...@yahoo.com Hello Justin, Thanks for your patient reply I would like to solvate my molecules with specific number of water molecules what option is a suitable to do that ? in editconf with regards S.Vidhya sankar -- 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 -- Nguyen Van Cuong PhD student - Curtin University of Technology Mobile: (+61) 452213981 -- 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 -shell
shivangi nangia wrote: Hi All, I have a question about genbox -shell option. The online manual says: *-shell*real0 thickness of optional water layer around solute The value specified for -shell option, example 3, produces a sphere with radius 3 nm or diameter 3 nm? Probably a radius. You can find out yourself by trying it. -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 question
Fabian Casteblanco wrote: Hello, I was wondering if someone can help me with a general genbox question. I have been using the command line: genbox -ci octanol.gro -nmol 1000 -box 5 5 5 -o prop_1000.gro to fill a box with 1000 molecules of octanol. With the smaller n-alcohols, it worked fine but as I started using 1-butanol, 1-pentanol, (longer carbon chains) up to octanol, Gromacs sometimes ends the command with a 'Killedin-Solvent overlap' line at the very end. Sometimes increasing the box size helped, but for 1-pentanol, even 7 7 7 box size didn't work. Also, do these killed runs take up some sort of space. My memory space decreases a little bit even on failed runs. Generating random boxes in this way requires lots of memory and is prone to failure. A useful strategy is to overestimate the size of the box so that genbox doesn't have to do too many iterations to place all of the molecules, then run a nice, long equilibration to get the box vectors (and therefore density, etc) correct. -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 question
Justin A. Lemkul wrote: Fabian Casteblanco wrote: Hello, I was wondering if someone can help me with a general genbox question. I have been using the command line: genbox -ci octanol.gro -nmol 1000 -box 5 5 5 -o prop_1000.gro to fill a box with 1000 molecules of octanol. With the smaller n-alcohols, it worked fine but as I started using 1-butanol, 1-pentanol, (longer carbon chains) up to octanol, Gromacs sometimes ends the command with a 'Killedin-Solvent overlap' line at the very end. Sometimes increasing the box size helped, but for 1-pentanol, even 7 7 7 box size didn't work. Also, do these killed runs take up some sort of space. My memory space decreases a little bit even on failed runs. Generating random boxes in this way requires lots of memory and is prone to failure. A useful strategy is to overestimate the size of the box so that genbox doesn't have to do too many iterations to place all of the molecules, then run a nice, long equilibration to get the box vectors (and therefore density, etc) correct. A more reliable method is probably genconf: genconf -f molecule.gro -nbox 10 10 10 -o box.gro You'll get 1000 molecules every time and the box size should be sensible. Then proceed with equilibration. -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 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
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
Re: [gmx-users] Genbox command question
Fabian Casteblanco wrote: Hello, I'm trying to place 1000 molecules of 1-propanol using CHARMM FF parameters in a -box 6 6 6. After minimization, I realized that for a single molecule, the potential was slightly above 0, '+24 kJ/mol' to be exact, with electrostatic coloumb potential the greatest contributor. I used the same thing with OPLSA FF parameters and got a '+3 kJ/mol'. I realize that when I place 1000 of these molecules, the potential will be very high since the potentials are positive to begin with. When I placed 1000 molecules using: This is not necessarily true. Isolated molecules can have positive potential energies due to unsatisfied interactions, but in a condensed phase, the presence of other molecules produces negative energies due to favorable van der Waals and hydrogen bonding interactions. - genbox -ci propanol.gro -nmol 1000 -box 6 6 6 -o prop1000.gro I resulted with a box full of 1000 molecules in that specific box size on gromacs 4.0.1. I did the same on the latest gromacs 4.5 but it ended up taking longer and the last line stating 'killed'. I redid it with a box 7 7 7 and it worked on gromacs 4.5. However, after I energy minimized both 1000 molecules (box 6 6 6 on gromacs 4.0.1) and (box 7 7 7 on gromacs 4.5), the first gave me a large negative potential energy (-6000 kJ/mol) after taking a long time and the Simulations with version 4.0.1 will be extremely slow due to a critical bug that was introduced. You should not use version 4.0.1; it was removed from the website within hours of its release due to series performance problems. second box gave me a somewhat large 2*10^3 kJ/mol. I am still new to A more expanded system will have unsatisfied interactions, thus positive energy. Gromacs but I'm confused on why a certain box size worked on one version of gromacs and the other didnt. I assume that the difference That's hard to pinpoint. If you have a 7-nm cubic box, gentle equilibration should produce a reasonable density and a much lower potential. in potential energies is since the 2nd box has way more space for these molecules therefore they are not as well equilibrated as the more compact box of size 6 6 6. Why does my box size that worked on Energy minimization and equilibration dynamics are different. A more dense system is simply more favorable. You can certainly achieve an equivalent result with proper NPT equilibration. -Justin gromacs4.0.1 work and on 4.5 it states killed as the last line and only works redoing it with a bigger box size. Thank you so much for your time and help ahead of time. -- Best regards, Fabian F. Casteblanco Rutgers University -- Chemical Engineering PhD Student C: +908 917 0723 E: fabian.castebla...@gmail.com -- 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
leila separdar wrote: I have .gro and .top of a nanoparticle at temperature 1K and I want to add the simulation box some other atomes at temperature 300K. is there any body knows how can I do it. I have used (genbox -cp nanoparticle.gro -ci otheratom.gro -p nanoparticle.top -o out) but it add more than atomes than I expect for example if there is 600 other atomes in otheratom,gro file this command add 2000 atomes to simulation box and also nanoparticle.top does not update. thanks in advance The -ci option should be used in conjunction with -nmol, and the configuration contained in -ci (I believe) cannot contain multiple molecules. If you want 600 molecules/atom to be inserted, provide a configuration of a single molecule/atom and specify -nmol 600. With respect to the topology not being updated, that is to be expected. The -p option only works for water (unfortunately). -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 error
Rini Gupta wrote: Dear gmx users, I am using gromacs (version 4.0.7) to setup a 2-butoxyethanol-water simulation. I created topology and coordinate file (.pdb) for BE using AUTOMATED TOPOLOGY BUILDER server. It created a topology file (for united atom) compatible with GROMOS ffG53a6 forcefield. I want to generate a box containing 20 BE and 480 water molecules using genbox but it fails to do so. It generates a box only with 1 BE instead of 20 but successfully adding requested no. of water molecules. I used the following command: genbox_d_mpi -cp conf.gro -cs spc216.gro -p topol.top -box 2.7 2.7 2.7 -ci conf.gro -nmol 19 -maxsol 480 -o out.gro Do the -ci and -cs steps separately and see if that gives you the proper output. I have found that the two are incompatible, but in theory, I don't know why one couldn't do everything in one step. -Justin Then I got the mesaage: Reading solute configuration UNITED ATOM STRUCTURE FOR MOLECULE Containing 9 atoms in 1 residues Initialising van der waals distances... Reading molecule configuration UNITED ATOM STRUCTURE FOR MOLECULE Containing 9 atoms in 1 residue Initialising van der waals distances... Try 5699 Added 0 molecules (out of 19 requested) of G2 Reading solvent configuration 216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984 solvent configuration contains 648 atoms in 216 residues Initialising van der waals distances... Will generate new solvent configuration of 2x2x2 boxes Generating configuration Sorting configuration Found 1 molecule type: SOL ( 3 atoms): 1728 residues Calculating Overlap... box_margin = 0.315 Removed 1992 atoms that were outside the box Neighborsearching with a cut-off of 0.45 Table routines are used for coulomb: FALSE Table routines are used for vdw: FALSE Cut-off's: NS: 0.45 Coulomb: 0.45 LJ: 0.45 System total charge: 0.000 Grid: 8 x 8 x 8 cells Succesfully made neighbourlist nri = 10648, nrj = 270745 Checking Protein-Solvent overlap: tested 509 pairs, removed 72 atoms. Checking Solvent-Solvent overlap: tested 39413 pairs, removed 738 atoms. Added 480 molecules Generated solvent containing 1440 atoms in 480 residues Writing generated configuration to out.gro While searching through mailing list I tried to do this in two separate steps i.e. but using -ci -nmol option and then solvating the box using -cs spc216.gro, but problem remain the same. I also tried increasing -try option and increasing the box size but still it is creating box with only one solute BE instead od 20. Can anyone please tell me what I am doing wrong here. I using following topology file: [ moleculetype ] ; Name nrexcl G269 3 [ atoms ] ; nr type resnr resid atom cgnr charge mass total_charge 1 OE 1 G2 OE 1 -0.345 15.9994 2 CH2 1 G2 C 1 0.151 14.0270 3 CH2 1 G2 C 1 0.194 14.0270 ; 0.000 4 CH2 1 G2 C 2 0.231 14.0270 5 OA 1 G2 O 2 -0.617 15.9994 6 H 1 G2 H 2 0.386 1.0080 ; 0.000 7 CH2 1 G2 C 3 -0.035 14.0270 8 CH2 1 G2 C 3 0.143 14.0270 9 CH3 1 G2 CA 3 -0.108 15.0350 ; -0.000 ; total charge of the molecule: 0.000 [ bonds ] ; ai aj funct c0 c1 1 2 2 0.1430 8.1800e+06 1 3 2 0.1430 8.1800e+06 2 4 2 0.1520 5.4300e+06 3 7 2 0.1520 5.4300e+06 4 5 2 0.1430 8.1800e+06 5 6 2 0.1000 2.3200e+07 7 8 2 0.1530 7.1500e+06 8 9 2 0.1530 7.1500e+06 [ pairs ] ; ai aj funct ; all 1-4 pairs but the ones excluded in GROMOS itp 1 5 1 1 8 1 2 6 1 2 7 1 3 4 1 3 9 1 [ angles ] ; ai aj ak funct angle fc 2 1 3 2 109.50 380.00 1 2 4 2 109.50 320.00 1 3 7 2 109.50 320.00 2 4 5 2 111.00 530.00 4 5 6 2 108.53 443.00 3 7 8 2 111.00 530.00 7 8 9 2 111.00 530.00 [ dihedrals ] ; GROMOS improper dihedrals ; ai aj ak al funct angle fc [ dihedrals ] ; ai aj ak al funct ph0 cp mult 3 1 2 4 1 0.00 1.26 3 2 1 3 7 1 0.00 1.26 3 1 2 4 5 1 0.00 2.53 3 1 3 7 8 1 0.00 3.77 3 2 4 5 6 1 0.00 1.26 3 3 7 8 9 1 0.00 3.77 3 [ exclusions ] ; ai aj funct ; GROMOS 1-4 exclusions Thanks and Regards, Rini Dr. Rini Gupta Postdoctoral Fellow University of British Columbia Vancouver http://sigads.rediff.com/RealMedia/ads/click_nx.ads/www.rediffmail.com/signatureline.htm@Middle? -- 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 error
On 12/02/2011 7:51 AM, Rini Gupta wrote: Dear gmx users, I am using gromacs (version 4.0.7) to setup a 2-butoxyethanol-water simulation. I created topology and coordinate file (.pdb) for BE using AUTOMATED TOPOLOGY BUILDER server. It created a topology file (for united atom) compatible with GROMOS ffG53a6 forcefield. I want to generate a box containing 20 BE and 480 water molecules using genbox but it fails to do so. It generates a box only with 1 BE instead of 20 but successfully adding requested no. of water molecules. I used the following command: genbox_d_mpi -cp conf.gro -cs spc216.gro -p topol.top -box 2.7 2.7 2.7 -ci conf.gro -nmol 19 -maxsol 480 -o out.gro Then I got the mesaage: Reading solute configuration UNITED ATOM STRUCTURE FOR MOLECULE Containing 9 atoms in 1 residues Initialising van der waals distances... Reading molecule configuration UNITED ATOM STRUCTURE FOR MOLECULE Containing 9 atoms in 1 residue Initialising van der waals distances... Try 5699 Added 0 molecules (out of 19 requested) of G2 Reading solvent configuration 216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984 solvent configuration contains 648 atoms in 216 residues Initialising van der waals distances... Will generate new solvent configuration of 2x2x2 boxes Generating configuration Sorting configuration Found 1 molecule type: SOL ( 3 atoms): 1728 residues Calculating Overlap... box_margin = 0.315 Removed 1992 atoms that were outside the box Neighborsearching with a cut-off of 0.45 Table routines are used for coulomb: FALSE Table routines are used for vdw: FALSE Cut-off's: NS: 0.45 Coulomb: 0.45 LJ: 0.45 System total charge: 0.000 Grid: 8 x 8 x 8 cells Succesfully made neighbourlist nri = 10648, nrj = 270745 Checking Protein-Solvent overlap: tested 509 pairs, removed 72 atoms. Checking Solvent-Solvent overlap: tested 39413 pairs, removed 738 atoms. Added 480 molecules Generated solvent containing 1440 atoms in 480 residues Writing generated configuration to out.gro While searching through mailing list I tried to do this in two separate steps i.e. but using -ci -nmol option and then solvating the box using -cs spc216.gro, but problem remain the same. I also tried increasing -try option and increasing the box size but still it is creating box with only one solute BE instead od 20. You're definitely trying to do too many things in one operation. I suggest 1. Use editconf to define a suitably big box around a single BE molecule. 2. Use genbox -ci -nmol 19 3. Use genbox -cs -cp Or use genconf -shuffle to replace 1 and 2 (but this is less random) Mark Can anyone please tell me what I am doing wrong here. I using following topology file: [ moleculetype ] ; Name nrexcl G269 3 [ atoms ] ; nr type resnr resid atom cgnr charge mass total_charge 1 OE 1 G2 OE 1 -0.345 15.9994 2 CH2 1 G2 C 1 0.151 14.0270 3 CH2 1 G2 C 1 0.194 14.0270 ; 0.000 4 CH2 1 G2 C 2 0.231 14.0270 5 OA 1 G2 O 2 -0.617 15.9994 6 H 1 G2 H 2 0.386 1.0080 ; 0.000 7 CH2 1 G2 C 3 -0.035 14.0270 8 CH2 1 G2 C 3 0.143 14.0270 9 CH3 1 G2 CA 3 -0.108 15.0350 ; -0.000 ; total charge of the molecule: 0.000 [ bonds ] ; ai aj funct c0 c1 1 2 2 0.1430 8.1800e+06 1 3 2 0.1430 8.1800e+06 2 4 2 0.1520 5.4300e+06 3 7 2 0.1520 5.4300e+06 4 5 2 0.1430 8.1800e+06 5 6 2 0.1000 2.3200e+07 7 8 2 0.1530 7.1500e+06 8 9 2 0.1530 7.1500e+06 [ pairs ] ; ai aj funct ; all 1-4 pairs but the ones excluded in GROMOS itp 1 5 1 1 8 1 2 6 1 2 7 1 3 4 1 3 9 1 [ angles ] ; ai aj ak funct angle fc 2 1 3 2 109.50 380.00 1 2 4 2 109.50 320.00 1 3 7 2 109.50 320.00 2 4 5 2 111.00 530.00 4 5 6 2 108.53 443.00 3 7 8 2 111.00 530.00 7 8 9 2 111.00 530.00 [ dihedrals ] ; GROMOS improper dihedrals ; ai aj ak al funct angle fc [ dihedrals ] ; ai aj ak al funct ph0 cp mult 3 1 2 4 1 0.00 1.26 3 2 1 3 7 1 0.00 1.26 3 1 2 4 5 1 0.00 2.53 3 1 3 7 8 1 0.00 3.77 3 2 4 5 6 1 0.00 1.26 3 3 7 8 9 1 0.00 3.77 3 [ exclusions ] ; ai aj funct ; GROMOS 1-4 exclusions Thanks and Regards, Rini Dr. Rini Gupta Postdoctoral Fellow University of British Columbia Vancouver http://sigads.rediff.com/RealMedia/ads/click_nx.ads/www.rediffmail.com/signatureline.htm@Middle? -- 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 error
On 12/02/2011 12:22 PM, Justin A. Lemkul wrote: Do the -ci and -cs steps separately and see if that gives you the proper output. I have found that the two are incompatible, but in theory, I don't know why one couldn't do everything in one step. It can depend on the assumptions about the purpose of -cs and -ci. If -ci is being used to insert some ions or small molecules then you want to do -cs first lest you create larger interstices via the VDW exclusions. If -ci inserts large molecules, then you want to do that first. The observations of the OP suggest the former is implemented. Mark -- 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 error
Hello Mark, Thanks for the reply. I tried to first make a box using editconf editconf_d_mpi -f conf.gro -o be.gro -bt cubic -box 2.7 2.7 2.7 Box is successfully created and then I use genbox_d_mpi -cp be.gro -p topol.top -ci be.gro -nmol 19 -o out.gro still, I am getting only one BE molecule instead of 19. What can I do now? Is there possibilty that my .gro file is not correct. Best Regards, Rini On Sat, 12 Feb 2011 06:58:49 +0530 wrote On 12/02/2011 7:51 AM, Rini Gupta wrote: Dear gmx users, I am using gromacs (version 4.0.7) to setup a 2-butoxyethanol-water simulation. I created topology and coordinate file (.pdb) for BE using AUTOMATED TOPOLOGY BUILDER server. It created a topology file (for united atom) compatible with GROMOS ffG53a6 forcefield. I want to generate a box containing 20 BE and 480 water molecules using genbox but it fails to do so. It generates a box only with 1 BE instead of 20 but successfully adding requested no. of water molecules. I used the following command: genbox_d_mpi -cp conf.gro -cs spc216.gro -p topol.top -box 2.7 2.7 2.7 -ci conf.gro -nmol 19 -maxsol 480 -o out.gro Then I got the mesaage: Reading solute configuration UNITED ATOM STRUCTURE FOR MOLECULE Containing 9 atoms in 1 residues Initialising van der waals distances... Reading molecule configuration UNITED ATOM STRUCTURE FOR MOLECULE Containing 9 atoms in 1 residue Initialising van der waals distances... Try 5699 Added 0 molecules (out of 19 requested) of G2 Reading solvent configuration 216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984 solvent configuration contains 648 atoms in 216 residues Initialising van der waals distances... Will generate new solvent configuration of 2x2x2 boxes Generating configuration Sorting configuration Found 1 molecule type: SOL ( 3 atoms): 1728 residues Calculating Overlap... box_margin = 0.315 Removed 1992 atoms that were outside the box Neighborsearching with a cut-off of 0.45 Table routines are used for coulomb: FALSE Table routines are used for vdw: FALSE Cut-off's: NS: 0.45 Coulomb: 0.45 LJ: 0.45 System total charge: 0.000 Grid: 8 x 8 x 8 cells Succesfully made neighbourlist nri = 10648, nrj = 270745 Checking Protein-Solvent overlap: tested 509 pairs, removed 72 atoms. Checking Solvent-Solvent overlap: tested 39413 pairs, removed 738 atoms. Added 480 molecules Generated solvent containing 1440 atoms in 480 residues Writing generated configuration to out.gro While searching through mailing list I tried to do this in two separate steps i.e. but using -ci -nmol option and then solvating the box using -cs spc216.gro, but problem remain the same. I also tried increasing -try option and increasing the box size but still it is creating box with only one solute BE instead od 20. You're definitely trying to do too many things in one operation. I suggest 1. Use editconf to define a suitably big box around a single BE molecule. 2. Use genbox -ci -nmol 19 3. Use genbox -cs -cp Or use genconf -shuffle to replace 1 and 2 (but this is less random) Mark Can anyone please tell me what I am doing wrong here. I using following topology file: [ moleculetype ] ; Name nrexcl G269 3 [ atoms ] ; nr type resnr resid atom cgnr charge mass total_charge 1 OE 1 G2 OE 1 -0.345 15.9994 2 CH2 1 G2 C 1 0.151 14.0270 3 CH2 1 G2 C 1 0.194 14.0270 ; 0.000 4 CH2 1 G2 C 2 0.231 14.0270 5 OA 1 G2 O 2 -0.617 15.9994 6 H 1 G2 H 2 0.386 1.0080 ; 0.000 7 CH2 1 G2 C 3 -0.035 14.0270 8 CH2 1 G2 C 3 0.143 14.0270 9 CH3 1 G2 CA 3 -0.108 15.0350 ; -0.000 ; total charge of the molecule: 0.000 [ bonds ] ; ai aj funct c0 c1 1 2 2 0.1430 8.1800e+06 1 3 2 0.1430 8.1800e+06 2 4 2 0.1520 5.4300e+06 3 7 2 0.1520 5.4300e+06 4 5 2 0.1430 8.1800e+06 5 6 2 0.1000 2.3200e+07 7 8 2 0.1530 7.1500e+06 8 9 2 0.1530 7.1500e+06 [ pairs ] ; ai aj funct ; all 1-4 pairs but the ones excluded in GROMOS itp 1 5 1 1 8 1 2 6 1 2 7 1 3 4 1 3 9 1 [ angles ] ; ai aj ak funct angle fc 2 1 3 2 109.50 380.00 1 2 4 2 109.50 320.00 1 3 7 2 109.50 320.00 2 4 5 2 111.00 530.00 4 5 6 2 108.53 443.00 3 7 8 2 111.00 530.00 7 8
Re: [gmx-users] genbox error
On 12/02/2011 12:51 PM, Rini Gupta wrote: Hello Mark, Thanks for the reply. I tried to first make a box using editconf editconf_d_mpi -f conf.gro -o be.gro -bt cubic -box 2.7 2.7 2.7 Box is successfully created and then I use genbox_d_mpi -cp be.gro -p topol.top -ci be.gro -nmol 19 -o out.gro still, I am getting only one BE molecule instead of 19. Hmm that's strange. What was the terminal output? Mark What can I do now? Is there possibilty that my .gro file is not correct. Best Regards, Rini On Sat, 12 Feb 2011 06:58:49 +0530 wrote On 12/02/2011 7:51 AM, Rini Gupta wrote: Dear gmx users, I am using gromacs (version 4.0.7) to setup a 2-butoxyethanol-water simulation. I created topology and coordinate file (.pdb) for BE using AUTOMATED TOPOLOGY BUILDER server. It created a topology file (for united atom) compatible with GROMOS ffG53a6 forcefield. I want to generate a box containing 20 BE and 480 water molecules using genbox but it fails to do so. It generates a box only with 1 BE instead of 20 but successfully adding requested no. of water molecules. I used the following command: genbox_d_mpi -cp conf.gro -cs spc216.gro -p topol.top -box 2.7 2.7 2.7 -ci conf.gro -nmol 19 -maxsol 480 -o out.gro Then I got the mesaage: Reading solute configuration UNITED ATOM STRUCTURE FOR MOLECULE Containing 9 atoms in 1 residues Initialising van der waals distances... Reading molecule configuration UNITED ATOM STRUCTURE FOR MOLECULE Containing 9 atoms in 1 residue Initialising van der waals distances... Try 5699 Added 0 molecules (out of 19 requested) of G2 Reading solvent configuration 216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984 solvent configuration contains 648 atoms in 216 residues Initialising van der waals distances... Will generate new solvent configuration of 2x2x2 boxes Generating configuration Sorting configuration Found 1 molecule type: SOL ( 3 atoms): 1728 residues Calculating Overlap... box_margin = 0.315 Removed 1992 atoms that were outside the box Neighborsearching with a cut-off of 0.45 Table routines are used for coulomb: FALSE Table routines are used for vdw: FALSE Cut-off's: NS: 0.45 Coulomb: 0.45 LJ: 0.45 System total charge: 0.000 Grid: 8 x 8 x 8 cells Succesfully made neighbourlist nri = 10648, nrj = 270745 Checking Protein-Solvent overlap: tested 509 pairs, removed 72 atoms. Checking Solvent-Solvent overlap: tested 39413 pairs, removed 738 atoms. Added 480 molecules Generated solvent containing 1440 atoms in 480 residues Writing generated configuration to out.gro While searching through mailing list I tried to do this in two separate steps i.e. but using -ci -nmol option and then solvating the box using -cs spc216.gro, but problem remain the same. I also tried increasing -try option and increasing the box size but still it is creating box with only one solute BE instead od 20. You're definitely trying to do too many things in one operation. I suggest 1. Use editconf to define a suitably big box around a single BE molecule. 2. Use genbox -ci -nmol 19 3. Use genbox -cs -cp Or use genconf -shuffle to replace 1 and 2 (but this is less random) Mark Can anyone please tell me what I am doing wrong here. I using following topology file: [ moleculetype ] ; Name nrexcl G269 3 [ atoms ] ; nr type resnr resid atom cgnr charge mass total_charge 1 OE 1 G2 OE 1 -0.345 15.9994 2 CH2 1 G2 C 1 0.151 14.0270 3 CH2 1 G2 C 1 0.194 14.0270 ; 0.000 4 CH2 1 G2 C 2 0.231 14.0270 5 OA 1 G2 O 2 -0.617 15.9994 6 H 1 G2 H 2 0.386 1.0080 ; 0.000 7 CH2 1 G2 C 3 -0.035 14.0270 8 CH2 1 G2 C 3 0.143 14.0270 9 CH3 1 G2 CA 3 -0.108 15.0350 ; -0.000 ; total charge of the molecule: 0.000 [ bonds ] ; ai aj funct c0 c1 1 2 2 0.1430 8.1800e+06 1 3 2 0.1430 8.1800e+06 2 4 2 0.1520 5.4300e+06 3 7 2 0.1520 5.4300e+06 4 5 2 0.1430 8.1800e+06 5 6 2 0.1000 2.3200e+07 7 8 2 0.1530 7.1500e+06 8 9 2 0.1530 7.1500e+06 [ pairs ] ; ai aj funct ; all 1-4 pairs but the ones excluded in GROMOS itp 1 5 1 1 8 1 2 6 1 2 7 1 3 4 1 3 9 1 [ angles ] ; ai aj ak funct angle fc 2 1 3 2 109.50 380.00 1 2 4 2 109.50 320.00 1 3 7 2 109.50 320.00 2 4 5 2 111.00 530.00 4 5 6 2 108.53 443.00 3 7 8 2 111.00 530.00 7 8 9 2 111.00 530.00 [ dihedrals ] ; GROMOS improper dihedrals ; ai aj ak al funct angle fc [ dihedrals ] ; ai aj ak al funct ph0 cp mult 3 1 2 4 1 0.00 1.26 3 2 1 3 7 1 0.00 1.26 3 1 2 4 5 1 0.00 2.53 3 1 3 7 8 1 0.00 3.77 3 2 4 5 6 1 0.00 1.26 3 3 7 8 9 1 0.00 3.77 3 [ exclusions ] ; ai aj funct ; GROMOS 1-4 exclusions Thanks and Regards, Rini Dr. Rini Gupta Postdoctoral Fellow University of British Columbia Vancouver -- 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!
Re: Re: [gmx-users] genbox error
Hi, I am getting following output after using editconf to create a box followed by genbox_d_mpi -cp be.gro -p topol.top -ci be.gro -nmol 2 -o out.gro This time i tried to insert just 2 molecules still the command is not working. --- Opening library file /global/software/gromacs/4.0.7/intel/share/gromacs/top/aminoacids.dat WARNING: masses will be determined based on residue and atom names, this can deviate from the real mass of the atom type Opening library file /global/software/gromacs/4.0.7/intel/share/gromacs/top/atommass.dat Entries in atommass.dat: 178 WARNING: vdwradii will be determined based on residue and atom names, this can deviate from the real mass of the atom type Opening library file /global/software/gromacs/4.0.7/intel/share/gromacs/top/vdwradii.dat Entries in vdwradii.dat: 28 Opening library file /global/software/gromacs/4.0.7/intel/share/gromacs/top/dgsolv.dat Entries in dgsolv.dat: 7 Opening library file /global/software/gromacs/4.0.7/intel/share/gromacs/top/electroneg.dat Entries in electroneg.dat: 71 Opening library file /global/software/gromacs/4.0.7/intel/share/gromacs/top/elements.dat Entries in elements.dat: 218 Reading solute configuration UNITED ATOM STRUCTURE FOR MOLECULE Containing 9 atoms in 1 residues Initialising van der waals distances... Reading molecule configuration UNITED ATOM STRUCTURE FOR MOLECULE Containing 9 atoms in 1 residue Initialising van der waals distances... Try 19 Added 0 molecules (out of 2 requested) of G2 Writing generated configuration to out.gro Back Off! I just backed up out.gro to ./#out.gro.1# UNITED ATOM STRUCTURE FOR MOLECULE Output configuration contains 9 atoms in 1 residues Volume : 19.683 (nm^3) Density: 8.94928 (g/l) Number of SOL molecules: 0 Processing topology -- Best Regards, Rini On Sat, 12 Feb 2011 08:07:27 +0530 wrote On 12/02/2011 12:51 PM, Rini Gupta wrote: Hello Mark, Thanks for the reply. I tried to first make a box using editconf editconf_d_mpi -f conf.gro -o be.gro -bt cubic -box 2.7 2.7 2.7 Box is successfully created and then I use genbox_d_mpi -cp be.gro -p topol.top -ci be.gro -nmol 19 -o out.gro still, I am getting only one BE molecule instead of 19. Hmm that's strange. What was the terminal output? Mark What can I do now? Is there possibilty that my .gro file is not correct. Best Regards, Rini On Sat, 12 Feb 2011 06:58:49 +0530 wrote On 12/02/2011 7:51 AM, Rini Gupta wrote: Dear gmx users, I am using gromacs (version 4.0.7) to setup a 2-butoxyethanol-water simulation. I created topology and coordinate file (.pdb) for BE using AUTOMATED TOPOLOGY BUILDER server. It created a topology file (for united atom) compatible with GROMOS ffG53a6 forcefield. I want to generate a box containing 20 BE and 480 water molecules using genbox but it fails to do so. It generates a box only with 1 BE instead of 20 but successfully adding requested no. of water molecules. I used the following command: genbox_d_mpi -cp conf.gro -cs spc216.gro -p topol.top -box 2.7 2.7 2.7 -ci conf.gro -nmol 19 -maxsol 480 -o out.gro Then I got the mesaage: Reading solute configuration UNITED ATOM STRUCTURE FOR MOLECULE Containing 9 atoms in 1 residues Initialising van der waals distances... Reading molecule configuration UNITED ATOM STRUCTURE FOR MOLECULE Containing 9 atoms in 1 residue Initialising van der waals distances... Try 5699 Added 0 molecules (out of 19 requested) of G2 Reading solvent configuration 216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984 solvent configuration contains 648 atoms in 216 residues Initialising van der waals distances... Will generate new solvent configuration of 2x2x2 boxes Generating configuration Sorting configuration Found 1 molecule type: SOL ( 3 atoms): 1728 residues Calculating Overlap... box_margin = 0.315 Removed 1992 atoms that were outside the box Neighborsearching with a cut-off of 0.45 Table routines are used for coulomb: FALSE Table
Re: [gmx-users] genbox generating acetonitrile box with holes
Diana Lousa wrote: Dear all, I tried to send this message earlier, but I had attached a pdb file and apparently it exceeded the size allowed in the mailing list and is awinting for the list moderator to evaluate it. I apologize if the message is sent twice. I am trying to solvate a protein in a box of acetonitrile using genbox. My initial solvent box is a cubic box containing 300 molecules of acetonitrile that has been equilibrated for 500 ps at constant P and T. I used the following protocol to generate the box: ### #create the box editconf -f protein.pdb -d 1.2 -o protein_in_box.pdb -bt dodecahedron #solvate genbox -cp protein_in_box.pdb -cs acetonitrile_eq.gro -o protein_in_acetonitrile.gro #convert the box to visualize it touch empty.mdp grompp -f empty.mdp -c protein_in_acetonitrile.gro -p 01_make_top/protein_ACN.top trjconv -f protein_in_acetonitrile.gro -o protein_in_acetonitrile.pdb -pbc atom -ur compact EOF 0 EOF ### After these steps I get a box that has holes and I can't understand why. How does the unmodified protin_in_acetonitrile.gro look? I couldn't send the final pdb file in attachment, if anyone thinks he/she can help and whishes to see the pdb file I will send it to your email. It would be far simpler to just post an image online, i.e. bullet point #4 here: http://www.gromacs.org/Support/Mailing_Lists#Mailing_List_Etiquette -Justin Thanks in advance. Diana -- Diana Lousa PhD student Protein Modeling Laboratory ITQB/UNL Oeiras, Portugal -- 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 generating acetonitrile box with holes
On 6/11/2010 12:54 AM, Diana Lousa wrote: Dear all, I tried to send this message earlier, but I had attached a pdb file and apparently it exceeded the size allowed in the mailing list and is awinting for the list moderator to evaluate it. I apologize if the message is sent twice. I am trying to solvate a protein in a box of acetonitrile using genbox. My initial solvent box is a cubic box containing 300 molecules of acetonitrile that has been equilibrated for 500 ps at constant P and T. I used the following protocol to generate the box: ### #create the box editconf -f protein.pdb -d 1.2 -o protein_in_box.pdb -bt dodecahedron #solvate genbox -cp protein_in_box.pdb -cs acetonitrile_eq.gro -o protein_in_acetonitrile.gro If you want to visualize a coordinate file, and you need a .pdb file for the purpose, simply write protein_in_acetonitrile.pdb in the above command. GROMACS rarely cares what coordinate file format you use, but its default is .gro format. See http://www.gromacs.org/Documentation/File_Formats/Coordinate_File#On_the_need_for_a_.gro_file. I've no idea whether the empty.mdp machinations below do work, but if they do, then I'd regard the fact that they do as evidence that GROMACS has a bug. #convert the box to visualize it touch empty.mdp grompp -f empty.mdp -c protein_in_acetonitrile.gro -p 01_make_top/protein_ACN.top trjconv -f protein_in_acetonitrile.gro -o protein_in_acetonitrile.pdb -pbc atom -ur compact EOF 0 EOF ### After these steps I get a box that has holes and I can't understand why. Do you know what trjconv -h says about -ur compact? Does this explain your holes? Mark I couldn't send the final pdb file in attachment, if anyone thinks he/she can help and whishes to see the pdb file I will send it to your email. Thanks in advance. Diana -- Diana Lousa PhD student Protein Modeling Laboratory ITQB/UNL Oeiras, Portugal -- 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 and martini, ethanol solvent
Pim Frederix wrote: Dear users, I'm trying to create a box with a number (64) of small peptide molecules (diphenylalanine) solved in ethanol for a Gromacs run with the Martini coarse-grain force field. I've created the box with the solute with the genbox -ci command: genbox -ci FFMM_cg.pdb -nmol 64 -box 5 5 5 -o FFMM_box.gro. This all seemed to work fine and I confirmed that it worked in VMD. However, when I try to fill the box with ethanol, this gives problems: genbox -cp FFMM_box.gro -cs ethanol_cg.pdb gets stuck at Reading solvent configuration solvent configuration contains 1 atoms in 1 residues (no error message, but just stops). 1 atom in 1 residue is correct for my pdb file, since ethanol is represented by 1 atom in Martini. I have tried to circumvent this problem by using the ci option again to add ethanol molecules 1 by 1. This kind of works, but if I try it for too many molecules (nmol 15000) it crashes as well with the message 'killed'. Also solving in ethanol that's not converted to coarse grain gets stuck (except from that it says 9 atoms in 1 residue). I have tried to solve it in the spc216 water, this works, so there must be something wrong with my pdb file for the solvent. I can see in other solvent gro/pdb files that there are usually a lot of solvent molecules in 1 file. Why is that and what can I do to make the ethanol box? Using -ci -nmol is prone to running out of memory, which is probably what's happening in your case. If you use genbox -cs, the configuration in the solvent coordinate file is expected to contain multiple atoms, or at the very least, multiple molecules. You can generate a box of CG ethanol using genconf -nbox (to make a grid), then equilibrate. Use this configuration as your solvent using genbox -cs. -Justin Thanks very much in advance, Pim PhD student University of Strathclyde Pure Applied Chemistry / Biomolecular and Chemical Physics -- 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 to generate box with isolated molecules...
Tandia, Adama wrote: Dears, I'm generating a box filled with NO3 molecules using Gromacs 3.3: Any particular reason you're using software that is five years old? Unless you've got a particular reason (i.e. continuity with older work), I'd strongly recommend upgrading to version 4.0.7 for all the newest features and a major speed upgrade. genbox -ci molecule.gro -p molecule.top -o bigbox.gro -box 4.0 4.0 4.0 -nmol 800 -vdwd 0.2 The file bigbox.gro is generated but molecules are entangled. This makes the geometry optimization to remove close contact impossible. Any suggestions? Have you tried a bigger box? Using a 5-nm box worked for me. When I tried the same command you did, my machine ran out of memory, so it's probably a rather complicated task and thus might not be a suitable application for this particular tool. Have you tried using genconf instead? With genconf you can easily build a lattice of NO3 that you can then equilibrate; genbox will try to randomize the configuration, but you can do it yourself with sufficient equilibration anyway. -Justin Thanks, Adama Adama Tandia, Corning INC, SP-TD-01-01 Corning NY 14831 USA, Tel: 607 248 1036 -GoogleVoice: 708 433 9430 -- 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/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/mailing_lists/users.php
Re: [gmx-users] genbox and water model
Sai Pooja wrote: Hi, I am using CHARMM forcefield with the tip3p. What input file(-cs) should i use to solvate the protein using the genbox command? The default is spc216.gro. What would be compatible with my system? I looked up the directory which has spc216.gro file. It has tip4p.gro file but for some reason doesnt have a tip3p.gro file. http://www.gromacs.org/Documentation/How-tos/TIP3P_coordinate_file -Justin Pooja -- Quaerendo Invenietis-Seek and you shall discover. -- 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/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/mailing_lists/users.php
Re: [gmx-users] genbox
shahid nayeem wrote: I was also trying to put more than one protein in one simulation box. I was able to do it with genconf but it appears that the addition is in very ordered manner if one looks .gro file in VMD. How can I add these protein in disordered random orientation. That's certainly what genconf does. You can apply a random rotation to your molecules with genconf -rot, but I don't know if that will remove any of the regularity in overall position. -Justin msnayeem On 4/20/10, *Justin A. Lemkul* jalem...@vt.edu mailto:jalem...@vt.edu wrote: fahimeh bafti wrote: Thanks :) but I couldn't manage with that, it makes the same error with editconf as well, the problem was related to having more than one residue inside insert.gro editconf should not have a problem placing multi-residue molecules within a box. That is its main function, so I can only assume you did something wrong. I did it at the end with genconf genconf -nbox 2 2 2 (as u want) -f file.gro -o file_replicate.pdb it will simply replicate the unit. That works. Glad you found a solution. -Justin Fahimeh Date: Tue, 20 Apr 2010 09:12:44 -0400 From: jalem...@vt.edu mailto:jalem...@vt.edu To: gmx-users@gromacs.org mailto:gmx-users@gromacs.org Subject: Re: [gmx-users] genbox fahimeh bafti wrote: Thank you Justin but I end up with a new error. now in the insert.pdp file I have a molecule which I need to add 4 copy of that inside the solute.pdb genbox_d -ci insert.pdb -nmol 4 -cp solute.pdb but it gave me: Fatal error: more then one residue in insert molecules program terminated Then you have two options: 1. Use the development (git) version of the code, which I believe can now deal with multi-residue molecules. 2. Use editconf to position all the components of your system. You could, I suppose, hack your insert.pdb to contain one residue (i.e., through renaming and renumbering) and then convert it back, but that sounds like a mess. Probably #2 is the easiest. -Justin Fahimeh Date: Tue, 20 Apr 2010 07:10:59 -0400 From: jalem...@vt.edu mailto:jalem...@vt.edu To: gmx-users@gromacs.org mailto:gmx-users@gromacs.org Subject: Re: [gmx-users] genbox fahimeh bafti Hello, I want to use a file.pdb which has 8 chain of polypeptide, each chain contains 6 residues. I need to expand it to 12 chains of 6 rsidues so I need to add 4 chains or in the other word 24 residues. I think I have to use genbox, so I make another copy of file.pdb and rename it to insert.pdb and i used this command, but it doesn't work. genbox -cp file.pdb -ci insert.pdb -nmole 24 -o out.gro can anybody help me? The implication with genbox -ci -nmol is that the coordinate file passed to -ci contains one molecule, and an additional -nmol molecules are inserted. So if you already have 8, you need a coordinate file with one polypeptide and then: genbox -ci insert.pdb -nmol 4 Note in the documentation that -nmol refers to the number of molecules, not a number of residues, which I think is the root of your problem. -Justin Fahimeh Hotmail: Trusted email with powerful SPAM protection. Sign up now. https://signup.live.com/signup.aspx?id=60969 -- 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
Re: [gmx-users] genbox
I was also trying to put more than one protein in one simulation box. I was able to do it with genconf but it appears that the addition is in very ordered manner if one looks .gro file in VMD. How can I add these protein in disordered random orientation. msnayeem On 4/20/10, Justin A. Lemkul jalem...@vt.edu wrote: fahimeh bafti wrote: Thanks :) but I couldn't manage with that, it makes the same error with editconf as well, the problem was related to having more than one residue inside insert.gro editconf should not have a problem placing multi-residue molecules within a box. That is its main function, so I can only assume you did something wrong. I did it at the end with genconf genconf -nbox 2 2 2 (as u want) -f file.gro -o file_replicate.pdb it will simply replicate the unit. That works. Glad you found a solution. -Justin Fahimeh Date: Tue, 20 Apr 2010 09:12:44 -0400 From: jalem...@vt.edu To: gmx-users@gromacs.org Subject: Re: [gmx-users] genbox fahimeh bafti wrote: Thank you Justin but I end up with a new error. now in the insert.pdp file I have a molecule which I need to add 4 copy of that inside the solute.pdb genbox_d -ci insert.pdb -nmol 4 -cp solute.pdb but it gave me: Fatal error: more then one residue in insert molecules program terminated Then you have two options: 1. Use the development (git) version of the code, which I believe can now deal with multi-residue molecules. 2. Use editconf to position all the components of your system. You could, I suppose, hack your insert.pdb to contain one residue (i.e., through renaming and renumbering) and then convert it back, but that sounds like a mess. Probably #2 is the easiest. -Justin Fahimeh Date: Tue, 20 Apr 2010 07:10:59 -0400 From: jalem...@vt.edu To: gmx-users@gromacs.org Subject: Re: [gmx-users] genbox fahimeh bafti Hello, I want to use a file.pdb which has 8 chain of polypeptide, each chain contains 6 residues. I need to expand it to 12 chains of 6 rsidues so I need to add 4 chains or in the other word 24 residues. I think I have to use genbox, so I make another copy of file.pdb and rename it to insert.pdb and i used this command, but it doesn't work. genbox -cp file.pdb -ci insert.pdb -nmole 24 -o out.gro can anybody help me? The implication with genbox -ci -nmol is that the coordinate file passed to -ci contains one molecule, and an additional -nmol molecules are inserted. So if you already have 8, you need a coordinate file with one polypeptide and then: genbox -ci insert.pdb -nmol 4 Note in the documentation that -nmol refers to the number of molecules, not a number of residues, which I think is the root of your problem. -Justin Fahimeh Hotmail: Trusted email with powerful SPAM protection. Sign up now. https://signup.live.com/signup.aspx?id=60969 -- 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/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/mailing_lists/users.php Hotmail: Trusted email with Microsoft’s powerful SPAM protection. Sign up now. https://signup.live.com/signup.aspx?id=60969 -- 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/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/mailing_lists/users.php
Re: [gmx-users] genbox
fahimeh bafti wrote: Hello, I want to use a file.pdb which has 8 chain of polypeptide, each chain contains 6 residues. I need to expand it to 12 chains of 6 rsidues so I need to add 4 chains or in the other word 24 residues. I think I have to use genbox, so I make another copy of file.pdb and rename it to insert.pdb and i used this command, but it doesn't work. genbox -cp file.pdb -ci insert.pdb -nmole 24 -o out.gro can anybody help me? The implication with genbox -ci -nmol is that the coordinate file passed to -ci contains one molecule, and an additional -nmol molecules are inserted. So if you already have 8, you need a coordinate file with one polypeptide and then: genbox -ci insert.pdb -nmol 4 Note in the documentation that -nmol refers to the number of molecules, not a number of residues, which I think is the root of your problem. -Justin Fahimeh Hotmail: Trusted email with powerful SPAM protection. Sign up now. https://signup.live.com/signup.aspx?id=60969 -- 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/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/mailing_lists/users.php
RE: [gmx-users] genbox
Thank you Justin but I end up with a new error. now in the insert.pdp file I have a molecule which I need to add 4 copy of that inside the solute.pdb genbox_d -ci insert.pdb -nmol 4 -cp solute.pdb but it gave me: Fatal error: more then one residue in insert molecules program terminated Fahimeh Date: Tue, 20 Apr 2010 07:10:59 -0400 From: jalem...@vt.edu To: gmx-users@gromacs.org Subject: Re: [gmx-users] genbox fahimeh bafti Hello, I want to use a file.pdb which has 8 chain of polypeptide, each chain contains 6 residues. I need to expand it to 12 chains of 6 rsidues so I need to add 4 chains or in the other word 24 residues. I think I have to use genbox, so I make another copy of file.pdb and rename it to insert.pdb and i used this command, but it doesn't work. genbox -cp file.pdb -ci insert.pdb -nmole 24 -o out.gro can anybody help me? The implication with genbox -ci -nmol is that the coordinate file passed to -ci contains one molecule, and an additional -nmol molecules are inserted. So if you already have 8, you need a coordinate file with one polypeptide and then: genbox -ci insert.pdb -nmol 4 Note in the documentation that -nmol refers to the number of molecules, not a number of residues, which I think is the root of your problem. -Justin Fahimeh Hotmail: Trusted email with powerful SPAM protection. Sign up now. https://signup.live.com/signup.aspx?id=60969 -- 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/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/mailing_lists/users.php _ Hotmail: Trusted email with Microsoft’s powerful SPAM protection. https://signup.live.com/signup.aspx?id=60969-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] genbox
fahimeh bafti wrote: Thank you Justin but I end up with a new error. now in the insert.pdp file I have a molecule which I need to add 4 copy of that inside the solute.pdb genbox_d -ci insert.pdb -nmol 4 -cp solute.pdb but it gave me: Fatal error: more then one residue in insert molecules program terminated Then you have two options: 1. Use the development (git) version of the code, which I believe can now deal with multi-residue molecules. 2. Use editconf to position all the components of your system. You could, I suppose, hack your insert.pdb to contain one residue (i.e., through renaming and renumbering) and then convert it back, but that sounds like a mess. Probably #2 is the easiest. -Justin Fahimeh Date: Tue, 20 Apr 2010 07:10:59 -0400 From: jalem...@vt.edu To: gmx-users@gromacs.org Subject: Re: [gmx-users] genbox fahimeh bafti Hello, I want to use a file.pdb which has 8 chain of polypeptide, each chain contains 6 residues. I need to expand it to 12 chains of 6 rsidues so I need to add 4 chains or in the other word 24 residues. I think I have to use genbox, so I make another copy of file.pdb and rename it to insert.pdb and i used this command, but it doesn't work. genbox -cp file.pdb -ci insert.pdb -nmole 24 -o out.gro can anybody help me? The implication with genbox -ci -nmol is that the coordinate file passed to -ci contains one molecule, and an additional -nmol molecules are inserted. So if you already have 8, you need a coordinate file with one polypeptide and then: genbox -ci insert.pdb -nmol 4 Note in the documentation that -nmol refers to the number of molecules, not a number of residues, which I think is the root of your problem. -Justin Fahimeh Hotmail: Trusted email with powerful SPAM protection. Sign up now. https://signup.live.com/signup.aspx?id=60969 -- 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/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/mailing_lists/users.php Hotmail: Trusted email with Microsoft’s powerful SPAM protection. Sign up now. https://signup.live.com/signup.aspx?id=60969 -- 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/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/mailing_lists/users.php
RE: [gmx-users] genbox
Thanks :) but I couldn't manage with that, it makes the same error with editconf as well, the problem was related to having more than one residue inside insert.gro I did it at the end with genconf genconf -nbox 2 2 2 (as u want) -f file.gro -o file_replicate.pdb it will simply replicate the unit. Fahimeh Date: Tue, 20 Apr 2010 09:12:44 -0400 From: jalem...@vt.edu To: gmx-users@gromacs.org Subject: Re: [gmx-users] genbox fahimeh bafti wrote: Thank you Justin but I end up with a new error. now in the insert.pdp file I have a molecule which I need to add 4 copy of that inside the solute.pdb genbox_d -ci insert.pdb -nmol 4 -cp solute.pdb but it gave me: Fatal error: more then one residue in insert molecules program terminated Then you have two options: 1. Use the development (git) version of the code, which I believe can now deal with multi-residue molecules. 2. Use editconf to position all the components of your system. You could, I suppose, hack your insert.pdb to contain one residue (i.e., through renaming and renumbering) and then convert it back, but that sounds like a mess. Probably #2 is the easiest. -Justin Fahimeh Date: Tue, 20 Apr 2010 07:10:59 -0400 From: jalem...@vt.edu To: gmx-users@gromacs.org Subject: Re: [gmx-users] genbox fahimeh bafti Hello, I want to use a file.pdb which has 8 chain of polypeptide, each chain contains 6 residues. I need to expand it to 12 chains of 6 rsidues so I need to add 4 chains or in the other word 24 residues. I think I have to use genbox, so I make another copy of file.pdb and rename it to insert.pdb and i used this command, but it doesn't work. genbox -cp file.pdb -ci insert.pdb -nmole 24 -o out.gro can anybody help me? The implication with genbox -ci -nmol is that the coordinate file passed to -ci contains one molecule, and an additional -nmol molecules are inserted. So if you already have 8, you need a coordinate file with one polypeptide and then: genbox -ci insert.pdb -nmol 4 Note in the documentation that -nmol refers to the number of molecules, not a number of residues, which I think is the root of your problem. -Justin Fahimeh Hotmail: Trusted email with powerful SPAM protection. Sign up now. https://signup.live.com/signup.aspx?id=60969 -- 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/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/mailing_lists/users.php Hotmail: Trusted email with Microsoft’s powerful SPAM protection. Sign up now. https://signup.live.com/signup.aspx?id=60969 -- 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/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/mailing_lists/users.php _ Hotmail: Powerful Free email with security by Microsoft. https://signup.live.com/signup.aspx?id=60969-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] genbox
fahimeh bafti wrote: Thanks :) but I couldn't manage with that, it makes the same error with editconf as well, the problem was related to having more than one residue inside insert.gro editconf should not have a problem placing multi-residue molecules within a box. That is its main function, so I can only assume you did something wrong. I did it at the end with genconf genconf -nbox 2 2 2 (as u want) -f file.gro -o file_replicate.pdb it will simply replicate the unit. That works. Glad you found a solution. -Justin Fahimeh Date: Tue, 20 Apr 2010 09:12:44 -0400 From: jalem...@vt.edu To: gmx-users@gromacs.org Subject: Re: [gmx-users] genbox fahimeh bafti wrote: Thank you Justin but I end up with a new error. now in the insert.pdp file I have a molecule which I need to add 4 copy of that inside the solute.pdb genbox_d -ci insert.pdb -nmol 4 -cp solute.pdb but it gave me: Fatal error: more then one residue in insert molecules program terminated Then you have two options: 1. Use the development (git) version of the code, which I believe can now deal with multi-residue molecules. 2. Use editconf to position all the components of your system. You could, I suppose, hack your insert.pdb to contain one residue (i.e., through renaming and renumbering) and then convert it back, but that sounds like a mess. Probably #2 is the easiest. -Justin Fahimeh Date: Tue, 20 Apr 2010 07:10:59 -0400 From: jalem...@vt.edu To: gmx-users@gromacs.org Subject: Re: [gmx-users] genbox fahimeh bafti Hello, I want to use a file.pdb which has 8 chain of polypeptide, each chain contains 6 residues. I need to expand it to 12 chains of 6 rsidues so I need to add 4 chains or in the other word 24 residues. I think I have to use genbox, so I make another copy of file.pdb and rename it to insert.pdb and i used this command, but it doesn't work. genbox -cp file.pdb -ci insert.pdb -nmole 24 -o out.gro can anybody help me? The implication with genbox -ci -nmol is that the coordinate file passed to -ci contains one molecule, and an additional -nmol molecules are inserted. So if you already have 8, you need a coordinate file with one polypeptide and then: genbox -ci insert.pdb -nmol 4 Note in the documentation that -nmol refers to the number of molecules, not a number of residues, which I think is the root of your problem. -Justin Fahimeh Hotmail: Trusted email with powerful SPAM protection. Sign up now. https://signup.live.com/signup.aspx?id=60969 -- 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/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/mailing_lists/users.php Hotmail: Trusted email with Microsoft’s powerful SPAM protection. Sign up now. https://signup.live.com/signup.aspx?id=60969 -- 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/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/mailing_lists/users.php Hotmail: Powerful Free email with security by Microsoft. Get it now. https://signup.live.com/signup.aspx?id=60969 -- 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
Re: [gmx-users] Genbox error message
On 28/01/10 13:06, Lum Nforbi wrote: Hello all, Can someone tell me the meaning of this error message after using the genbox command? Certainly not without more useful information - GROMACS version, simulation system size, actual command line. Even then, the best guess is probably that you're running genbox on a machine for which it wasn't compiled, or for which some shared libraries have been updated in an incompatible way. Try recompiling GROMACS if so. Mark *** glibc detected *** genbox: munmap_chunk(): invalid pointer: 0x095969c8 *** === Backtrace: = /lib/tls/i686/cmov/libc.so.6[0xb7e7c454] genbox[0x81195c4] === Memory map: 08048000-082be000 r-xp 08:01 4333977 /usr/local/gromacs/bin/genbox 082be000-082bf000 r-xp 00275000 08:01 4333977 /usr/local/gromacs/bin/genbox 082bf000-082c5000 rwxp 00276000 08:01 4333977 /usr/local/gromacs/bin/genbox 082c5000-082cb000 rwxp 082c5000 00:00 0 0958f000-099e9000 rwxp 0958f000 00:00 0 [heap] b7df3000-b7df4000 rwxp b7df3000 00:00 0 b7df4000-b7e09000 r-xp 08:01 3860700 /lib/tls/i686/cmov/libpthread-2.8.90.so http://libpthread-2.8.90.so b7e09000-b7e0a000 r-xp 00014000 08:01 3860700 /lib/tls/i686/cmov/libpthread-2.8.90.so http://libpthread-2.8.90.so b7e0a000-b7e0b000 rwxp 00015000 08:01 3860700 /lib/tls/i686/cmov/libpthread-2.8.90.so http://libpthread-2.8.90.so Aborted I appreciate your help. Lum -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] genbox error at futil.c
iulek wrote:
Hi!
I am a very beginner, trying to make some dynamics of a protein in a
water box, after doing some (web) tutorials. I googled first for this
(possibly simple) error, found one reference, but cannot see it,
possibly because the gromacs site is under changes.
I ran pdb2gmx and editconf. Then at genbox I get the error:
Processing topology
---
Program genbox, VERSION 4.0.5
Source code file: futil.c, line: 330
File input/output error:
RecA_nat_b4em.top
---
So is the topology in the current working directory?
-Justin
The command line is:
genbox -cp ${MOL}_in_box.gro -cs -p ${MOL}_b4em.top -o
${MOL}_b4em.gro eof genbox.log
eof
with variable MOL set to RecA_nat
The file RecA_nat_b4em.gro is output without problems.
I am using gromacs 4.0.5 under openSuSE 11.1.
Thanks,
Jorge
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--
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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Re: Re: [gmx-users] genbox error at futil.c
Thanks for replying.
Humm..., maybe I see now. As a beginner I intended to keep all files
produced and better inspect what happens in sequence, but I did not want
to use the conventional renaming. But it seems that for the topology
file, the common procedure is to keep always one only name through the
several steps, right? That is what I understand with
Option Filename Type Description
-p topol.top In/Out, Opt. Topology file
so, the same name for input and output, yet genbox renames the old
one according to the conventions (which in my script I could then
further re-rename).
And... genbox does need a previous topology file (RecA_nat_b4em.top
was intended to be the output file!).
Thanks, again.
Jorge
iulek wrote:
Hi!
I am a very beginner, trying to make some dynamics of a protein
in a water box, after doing some (web) tutorials. I googled first for
this (possibly simple) error, found one reference, but cannot see it,
possibly because the gromacs site is under changes.
I ran pdb2gmx and editconf. Then at genbox I get the error:
Processing topology
---
Program genbox, VERSION 4.0.5
Source code file: futil.c, line: 330
File input/output error:
RecA_nat_b4em.top
---
So is the topology in the current working directory?
-Justin
The command line is:
genbox -cp ${MOL}_in_box.gro -cs -p ${MOL}_b4em.top -o
${MOL}_b4em.gro eof genbox.log
eof
with variable MOL set to RecA_nat
The file RecA_nat_b4em.gro is output without problems.
I am using gromacs 4.0.5 under openSuSE 11.1.
Thanks,
Jorge
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Re: [gmx-users] genbox error at futil.c
iulek wrote:
Thanks for replying.
Humm..., maybe I see now. As a beginner I intended to keep all files
produced and better inspect what happens in sequence, but I did not want
to use the conventional renaming. But it seems that for the topology
file, the common procedure is to keep always one only name through the
several steps, right? That is what I understand with
You can keep the same name, or manually make your own backup copies along the
way (topol_orig.top, topol_after_sol.top, etc).
Option Filename Type Description
-p topol.top In/Out, Opt. Topology file
so, the same name for input and output, yet genbox renames the old
one according to the conventions (which in my script I could then
further re-rename).
Right, genbox will not make a new file for you, it simply processes the input
topology, which becomes the output once it is modified.
-Justin
And... genbox does need a previous topology file (RecA_nat_b4em.top
was intended to be the output file!).
Thanks, again.
Jorge
iulek wrote:
Hi!
I am a very beginner, trying to make some dynamics of a protein
in a water box, after doing some (web) tutorials. I googled first for
this (possibly simple) error, found one reference, but cannot see it,
possibly because the gromacs site is under changes.
I ran pdb2gmx and editconf. Then at genbox I get the error:
Processing topology
---
Program genbox, VERSION 4.0.5
Source code file: futil.c, line: 330
File input/output error:
RecA_nat_b4em.top
---
So is the topology in the current working directory?
-Justin
The command line is:
genbox -cp ${MOL}_in_box.gro -cs -p ${MOL}_b4em.top -o
${MOL}_b4em.gro eof genbox.log
eof
with variable MOL set to RecA_nat
The file RecA_nat_b4em.gro is output without problems.
I am using gromacs 4.0.5 under openSuSE 11.1.
Thanks,
Jorge
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--
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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Re: [gmx-users] Genbox problem with TIP4P water with OPLS
Hi Mark, I think 3.3.2, does it be fixed in 4.0? Chao On Wed, Feb 18, 2009 at 12:06 PM, Mark Abraham mark.abra...@anu.edu.auwrote: Chao Zhang wrote: Dear gmx-user, I try to build a pure water box in Gromacs, so I just solved one water as solute with genbox. When I use tip3p water, my scripts work well. But to switch to tip4p water, there seems a bug, I don't know whether people have noticed this or not. The system shows that it added 350 water but just write 349 water in topology file, therefore failed the test of grompp. Any suggestion? # Added 350 molecules Generated solvent containing 1400 atoms in 350 residues Writing generated configuration to test_sol.gro Back Off! I just backed up test_sol.gro to ./#test_sol.gro.5# salt in water Output configuration contains 1404 atoms in 351 residues Volume : 9.95267 (nm^3) Density: 1055.19 (g/l) Number of SOL molecules:350 Processing topology Adding line for 349 solvent molecules to topology file (test.top) What version of GROMACS is this? Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- Chao Zhang ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Genbox problem with TIP4P water with OPLS
Chao Zhang wrote: Hi Mark, I think 3.3.2, does it be fixed in 4.0? I don't know - I've not seen it reported. You should search the mailing list archives. There won't be any interest in diagnosing or fixing it within version 3.x, but if you can reproduce your result in 4.0.4, file a bugzilla from the GROMACS website and it'll get attention. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Genbox problem with TIP4P water with OPLS
On Thu, Feb 19, 2009 at 01:56:28AM +1100, Mark Abraham wrote: Chao Zhang wrote: Hi Mark, I think 3.3.2, does it be fixed in 4.0? I don't know - I've not seen it reported. You should search the mailing list archives. I've solvated with tip4p in 3.3cvs and 3.3.1, never had the problem. anyway, a `grep 'OW SOL' box.pdb | wc -l` will tell you how many solvent molecules you have. cheers, marc ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] genbox
Sunil Thapa wrote: Respectable Mark I am studying diffusion of oxygen in water. Can I specify the number of water molecules for a particular size of box. For example, I need to have 98 water molecules and 2 oxygen molecules in one solution. After that I need to increase the number of oxygen molecules and decrease the number of water molecules, viz, 10 oxygen molecules and 90 water molecules. What i have found so far is that genbox adds the number of water molecules according to the size of the box. For cubical box of 1.5nm it adds about 110 water molecules. Your help would be very helpful in this regard. genbox -h shows you that there is an option genbox -maxsol Sunil Kumar Thapa Tribhuvan University, Nepal ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. sp...@xray.bmc.uu.sesp...@gromacs.org http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] genbox -ci solute.gro -nmol N
Chih-Ying Lin wrote: Hi Originally, in the topol.top file = [molecule] solute 1 After the command: genbox -cp one_solute.gro -cs spc216.gro -ci one_solute.gro -nmol N -p topol.top in the topol.top file = [molecule] solute 1 solvent 5000 I think the flag -p topol.top in the genbox command did not do it correctly. I am considering the two possible modification on the topol.top file [molecule] solute (1+N) solvent 5000 [molecule] solute (1+N) solvent (5000 - N) Which one is correct? Depends, what's in the genbox output structure? Or, none of them is correct? What is the correct form of it? It is often easier to insert a molecule with -ci, then solvate in the next step (at least from a conceptual standpoint). I don't know how the code will handle it, but it should certainly clear up your confusion. -Justin Thank you Lin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant 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://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] genbox using tip5p water results in too few number of water molecules
JW Feng wrote: David, The results from using version 3.3.1 is different from version 3.3.2. In version 3.3.1, adding SOL OL 0 and executing genbox -cs tip5p.gro -box 1 1 1 created a box with 37 SOL molecules but the density is too high at 3072.87 g/L. In version 3.3.2, adding SOL OL 0 did not work. However, I added SOL LP0 to the end of vdwradii.dat and the resulting water box contained 37 SOL molecules. The density is incorrect at 2582.79 g/l. This box contains six more SOL molecules compared to a box created with TIP4P water. that is a coincidence. try with a larger box. the number is correct. JW On 10/7/07, David van der Spoel [EMAIL PROTECTED] wrote: JW Feng wrote: Hello, I used genbox (version 3.3.1 and 3.3.2) to create a 1nm box of SPC, TIP4P and TIP5P water with genbox -cs water model.gro -box 1 1 1. The TIP5P box contains half the number of water molecules compared to TIP4P and SPC. SPC: 33 SOL molecules, density=987.205 (g/l) TIP4P: 31 SOL molecules TIP5P: 15 SOL molecules Can anyone please explain this? How do I get genbox to create a box with the right number of TIP5P water molecules. Thanks, JW It is because of the name of the lone pairs (OL) which is interpreted as an oxygen atom. You can add OL in vdwradii.dat with radius 0 and try again. Please report whether it works, then I will fix it in further releases. -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED][EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] genbox using tip5p water results in too few number of water molecules
JW Feng wrote: Hello, I used genbox (version 3.3.1 and 3.3.2) to create a 1nm box of SPC, TIP4P and TIP5P water with genbox -cs water model.gro -box 1 1 1. The TIP5P box contains half the number of water molecules compared to TIP4P and SPC. SPC: 33 SOL molecules, density=987.205 (g/l) TIP4P: 31 SOL molecules TIP5P: 15 SOL molecules Can anyone please explain this? How do I get genbox to create a box with the right number of TIP5P water molecules. Thanks, JW It is because of the name of the lone pairs (OL) which is interpreted as an oxygen atom. You can add OL in vdwradii.dat with radius 0 and try again. Please report whether it works, then I will fix it in further releases. -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] genbox problem with micelle
If you have the center coordinates and your cell has a good radial symmetry, i would just write a script, checking the distance of each water to the center and then skipping everything below the radius of your cell. Cheers Martin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] genbox problem with micelle
Alif M Latif wrote: Dear GROMACS users and developers.. I'm trying to run MD simulation on a micelle structure, which i've built using Packmol. The problem is when i use genbox to solvate the system using SPC water, the water came inside the micelle, and my simulation didn't produce any significant changes to the structure (the behavior of lipids which are lipophilic should squeezed the water molecules outside the micelle structure). I'm wondering if i can tell genbox not to put water molecule inside the micelle...can i?.. :-p Thanks 4 reading...any comments and suggestion will be greatly appreciated.. A third alternative would be to increase the vdw radii, by copying vdwradii.dat to your working directory and increase the water radius. -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] genbox problem with micelle
Dear GROMACS users and developers.. I'm trying to run MD simulation on a micelle structure, which i've built using Packmol. The problem is when i use genbox to solvate the system using SPC water, the water came inside the micelle, and my simulation didn't produce any significant changes to the structure (the behavior of lipids which are lipophilic should squeezed the water molecules outside the micelle structure). I'm wondering if i can tell genbox not to put water molecule inside the micelle...can i?.. :-p genbox just uses vdw radii for different atom types to generate volumes that exclude waters. If your micelle (and I presume from the above that you have a micelle that is lipid-inside-surface water-outside-surface) has interstices that are large enough to admit waters, then genbox will place them there. Probably, an energy minimization of the micelle in vacuo will see it contract so that the lipids are pretty much close-packed, and hopefully this density will also be close to that for the micelle in solution. Alternatively, or if there are still holes that admit waters, you can make the radii of your lipid C and H atoms larger for the purposes of genbox using a modified gromacs/share/top/vdwradii.dat. Be careful later with the gentleness of your minimization and equilibration schemes else you'll generate large structural changes and thus bad contacts and LINCS errors, etc. Otherwise, you could get out a molecule visualization program like VMD, find the waters inside and delete them (you could script this with VMD, too). There's also a lesson here to look at your structure before you simulate to see that it looks how you expect it to. If you'd seen these waters, and knew for some reason that it would take longer than your simulation time to form an equilibrated micelle by excluding these waters, then you'd have known not to bother with this simulation, and fixed your problem without spending computer time needlessly. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Genbox problem ...
Kedar Potdar wrote: Hi friends, I have compiled Gromacs on native windows. The first two program in demo script (perl implementation of script “demo”) work fine but genbox displays following output Reading solute configuration Glycine aRginine prOline Methionine Alanine Cystine Serine Containing 145 atoms in 13 residues Initialising van der waals distances... Reading solvent configuration 216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984 solvent configuration contains 648 atoms in 216 residues Initialising van der waals distances... Will generate new solvent configuration of 2x2x2 boxes Generating configuration Sorting configuration Found 1 molecule type: SOL ( 3 atoms): 1728 residues Calculating Overlap... box_margin = 0.315 Removed 2895 atoms that were outside the box Succesfully made neighbourlist nri = 11448, nrj = 456822 Checking Protein-Solvent overlap: tested 4131 pairs, removed 228 atoms. Checking Solvent-Solvent overlap: tested 36954 pairs, removed 597 atoms. Added 488 molecules Generated solvent containing 1464 atoms in 488 residues Writing generated configuration to cpeptide_b4em.gro Glycine aRginine prOline Methionine Alanine Cystine Serine Output configuration contains 1609 atoms in 501 residues Volume : 17.1176 (nm^3) Density: 1002.99 (g/l) Number of SOL molecules:488 Processing topology Back Off! I just backed up cpeptide.top to ./#cpeptide.top.1# *Cpeptide.top file is of zero bytes now… and all further programs in the test fail after this.* * * Has anybody faced such problem before? What is remedy for this problem? Check the source code for opening of the file in genbox. It tries to append to the file, and the code for that may be different windows than under Unix. -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] Genbox problem ...
Yeah actually I got cause of the problem... :) I need to remove the topinput file before renaming TEMP_FILENM with topinput. Thanks... -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of David van der Spoel Sent: Tuesday, May 29, 2007 6:35 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Genbox problem ... Kedar Potdar wrote: Hi friends, I have compiled Gromacs on native windows. The first two program in demo script (perl implementation of script demo) work fine but genbox displays following output Reading solute configuration Glycine aRginine prOline Methionine Alanine Cystine Serine Containing 145 atoms in 13 residues Initialising van der waals distances... Reading solvent configuration 216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984 solvent configuration contains 648 atoms in 216 residues Initialising van der waals distances... Will generate new solvent configuration of 2x2x2 boxes Generating configuration Sorting configuration Found 1 molecule type: SOL ( 3 atoms): 1728 residues Calculating Overlap... box_margin = 0.315 Removed 2895 atoms that were outside the box Succesfully made neighbourlist nri = 11448, nrj = 456822 Checking Protein-Solvent overlap: tested 4131 pairs, removed 228 atoms. Checking Solvent-Solvent overlap: tested 36954 pairs, removed 597 atoms. Added 488 molecules Generated solvent containing 1464 atoms in 488 residues Writing generated configuration to cpeptide_b4em.gro Glycine aRginine prOline Methionine Alanine Cystine Serine Output configuration contains 1609 atoms in 501 residues Volume : 17.1176 (nm^3) Density: 1002.99 (g/l) Number of SOL molecules:488 Processing topology Back Off! I just backed up cpeptide.top to ./#cpeptide.top.1# *Cpeptide.top file is of zero bytes now. and all further programs in the test fail after this.* * * Has anybody faced such problem before? What is remedy for this problem? Check the source code for opening of the file in genbox. It tries to append to the file, and the code for that may be different windows than under Unix. -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] genbox give coord file more waters than top file
8 mar 2007 kl. 01.32 skrev Mark Abraham: Dear gromacs guys Why would genbox put more water molecules in my .gro file than in my .top file? I'm sure all I have to do is edit the number in my top file, but I have not had this happen before, does anyone know of a reason that this happens so I can fix my file? genbox doesn't read a top and produce that many solvent molecules. For a start, how does it know what shape you want them in? Read man genbox, choose what you want to do, apply genbox, and then edit your .top so the number of waters agrees with what genbox produced... not the other way around. Mark I'm not so sure about that. genbox *does* take a top file as an optional argument. genbox -h tells me: Finally, genbox will optionally remove lines from your topology file in which a number of solvent molecules is already added, and adds a line with the total number of solvent molecules in your coordinate file. I have never used this option, so I don't know exactly how it works, but I expect it to do what William wants it to do. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ Erik Marklund, PhD student Laboratory of Molecular Biophysics, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: +46 18 471 4537 fax: +46 18 511 755 [EMAIL PROTECTED] http://xray.bmc.uu.se/molbiophys ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] genbox give coord file more waters than top file
From: WILLIAM R WELCH [EMAIL PROTECTED] Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org To: gmx-users@gromacs.org Subject: [gmx-users] genbox give coord file more waters than top file Date: Wed, 07 Mar 2007 16:53:11 -0600 Dear gromacs guys Why would genbox put more water molecules in my .gro file than in my .top file? I'm sure all I have to do is edit the number in my top file, but I have not had this happen before, does anyone know of a reason that this happens so I can fix my file? I have seen this problem for the first time on our Gromacs workshop last week. I think the problem is that genbox does not recognize some crystal waters in your input coordinate file. genbox currently checks for SOL, WAT and HOH. What is the residue name of your crystal waters? The solution for the moment is to manually count the water molecules in the gro file and then correct the top file. Berk. _ Live Search, for accurate results! http://www.live.nl ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] genbox give coord file more waters than top file
8 mar 2007 kl. 01.32 skrev Mark Abraham: Dear gromacs guys Why would genbox put more water molecules in my .gro file than in my .top file? I'm sure all I have to do is edit the number in my top file, but I have not had this happen before, does anyone know of a reason that this happens so I can fix my file? genbox doesn't read a top and produce that many solvent molecules. For a start, how does it know what shape you want them in? Read man genbox, choose what you want to do, apply genbox, and then edit your .top so the number of waters agrees with what genbox produced... not the other way around. Mark I'm not so sure about that. genbox *does* take a top file as an optional argument. genbox -h tells me: Finally, genbox will optionally remove lines from your topology file in which a number of solvent molecules is already added, and adds a line with the total number of solvent molecules in your coordinate file. I have never used this option, so I don't know exactly how it works, but I expect it to do what William wants it to do. Maybe this works, I've never used it either... but the point is that the source of the information about how many waters to add comes from the genbox command line, not this .top file. I think William wanted the number of waters in his .top file to be added to his .gro file, and this is an ill-defined proposition. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] genbox give coord file more waters than top file
From: Mark Abraham [EMAIL PROTECTED] Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org To: Discussion list for GROMACS users gmx-users@gromacs.org Subject: Re: [gmx-users] genbox give coord file more waters than top file Date: Thu, 8 Mar 2007 22:27:01 +1100 (EST) 8 mar 2007 kl. 01.32 skrev Mark Abraham: Dear gromacs guys Why would genbox put more water molecules in my .gro file than in my .top file? I'm sure all I have to do is edit the number in my top file, but I have not had this happen before, does anyone know of a reason that this happens so I can fix my file? genbox doesn't read a top and produce that many solvent molecules. For a start, how does it know what shape you want them in? Read man genbox, choose what you want to do, apply genbox, and then edit your .top so the number of waters agrees with what genbox produced... not the other way around. Mark I'm not so sure about that. genbox *does* take a top file as an optional argument. genbox -h tells me: Finally, genbox will optionally remove lines from your topology file in which a number of solvent molecules is already added, and adds a line with the total number of solvent molecules in your coordinate file. I have never used this option, so I don't know exactly how it works, but I expect it to do what William wants it to do. Maybe this works, I've never used it either... but the point is that the source of the information about how many waters to add comes from the genbox command line, not this .top file. I think William wanted the number of waters in his .top file to be added to his .gro file, and this is an ill-defined proposition. Mark This depends. If the gro and top came out of pdb2gmx, pdb2gmx already recognized the water molecules and wrote the gro and top files. genbox is supposed to regonize these crystal waters in the gro and top file. Normally it would just add a line for the added water molecules. But genbox is so smart that it checks if the waters in the output configuration match the number in the orginal top plus the added waters, and it corrects the top if there is something wrong. I would guess that this is where the error occurs. Please file a bug report to bugzilla.gromacs.org with the gro and top file and the command line used for genbox. Berk. _ FREE pop-up blocking with the new Windows Live Toolbar - get it now! http://toolbar.msn.click-url.com/go/onm00200415ave/direct/01/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] genbox give coord file more waters than top file
Dear gromacs guys Why would genbox put more water molecules in my .gro file than in my .top file? I'm sure all I have to do is edit the number in my top file, but I have not had this happen before, does anyone know of a reason that this happens so I can fix my file? genbox doesn't read a top and produce that many solvent molecules. For a start, how does it know what shape you want them in? Read man genbox, choose what you want to do, apply genbox, and then edit your .top so the number of waters agrees with what genbox produced... not the other way around. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] genbox peptide-membrane simulation
Maite, The option -d sets a distance to be met on all sides, considering all the atoms to in the ouput selection. That's not what you want for a membrane now, is it? So, you don't want that option. You should have a box from the lipids anyway, I guess (used to equilibrate that system), just extend the z-coordinate (third number in the last row of the .gro file) such that your peptide fits in. Furthermore, molecules can't go out of the box, there is no outside! There's only wrapping from one side to the opposite one. Please read the manual and the mailing list regarding periodic boundary conditions (and setting up membrane-peptide simulations). Tsjerk On 2/2/07, maite lopez [EMAIL PROTECTED] wrote: Hi gromacs users: I'm simulating a peptide-dppc64 system. When i create my box with editconf program (editconf -f input.gro -o output.gro -bt triclinic -c -d 1.5) and i solvate, the molecule go out of the box. I used many kind of box and some box sizes. My system size is 4.936 4.408 and 10.503 nm. Should i use -d option with editconf? I've found in the gmx-users list and in many tutorials, it should be no less than 0.5. I don't want to solvate the system in x and y axes due to the interaction betwen lipids and water. I did it whit editconf -f input.gro -o output.gro -bt triclinic -c -box 4.936 4.408 12 , but i didn't use the -d option. Is that ok? So my question is: Can I do something whit -d and -box option of editconf program for resulting in a system that it doesn't solvate in x and y axes, and the molecule isn't out? I need to solvate in z axes. whould you please help me? best regard ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] genbox using TIP3P?--Nevermind
Nevermind, I made one using VMD, it solvated my protien just fine. - Original Message - From: WILLIAM R WELCH [EMAIL PROTECTED] Date: Friday, February 2, 2007 3:25 pm Subject: [gmx-users] genbox using TIP3P? To: Discussion list for GROMACS users gmx-users@gromacs.org Hello I would like to use the TIP3P model in my calculation, and I would like to be able to use genbox to solvate a pepetide, but there is no TIP3P.gro coordinate file in the program. I there such a coordinate file available? Will - Original Message - From: [EMAIL PROTECTED] Date: Friday, February 2, 2007 11:46 am Subject: [gmx-users] fitting procedure in g_rmsf To: gmx-users@gromacs.org Hello, I have a rather basic query. I want to know which atoms of the reference structure will be used for fitting , in g_rmsf program. In the program g_rms there are separate options for fitting and calcualation of rmsd. I wonder if it is possible for the user to select a set of atoms for fitting and calculate the rmsf over another range of atoms or the whole protein, similar as in g_rms program. Waiting for your suggessions. sridhar ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] genbox using TIP3P?
WILLIAM R WELCH wrote: Hello I would like to use the TIP3P model in my calculation, and I would like to be able to use genbox to solvate a pepetide, but there is no TIP3P.gro coordinate file in the program. I there such a coordinate file available? Any 3-point water model will be fine for generating solvent coordinates - the standard practice in GROMACS is to solvate with spc216.gro (per man genbox) and then in the .top file to #include tip3p.itp Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] genbox
Tamas Horvath wrote: Is it possible to maximise the water molecules to be inserted into the box? Define maximise. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] genbox
Tamas Horvath wrote: Can I define the maximum number of water molecules to be added by genebox. in 3.3.1 yes, -maxsol (use -h to see all options of any program) On 10/29/06, *Mark Abraham* [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] wrote: Tamas Horvath wrote: Is it possible to maximise the water molecules to be inserted into the box? Define maximise. Mark ___ gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] mailto:[EMAIL PROTECTED]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Genbox - Removal of Unwanted Waters
Arneh Babakhani wrote: Hello all, How do you remove unwanted waters (or how do you prevent genbox from placing unwanted waters) after you solvate by genbox? This problem was posted once before, http://www.gromacs.org/pipermail/gmx-users/2005-December/018997.html but it doesn't seem like it was resolved. Is there an easy way to do this (aside from going into the .gro file and manually deleting the unwanted waters!) genbox 3.3.1 has an option to set the maximum number of waters. Thanks, Arneh ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Genbox - Removal of Unwanted Waters
Thanks for the input. Is there a way to restrict the water from a certain space (in other words, to confine it a certain location)? Thanks, Arneh David van der Spoel wrote: Arneh Babakhani wrote: Hello all, How do you remove unwanted waters (or how do you prevent genbox from placing unwanted waters) after you solvate by genbox? This problem was posted once before, http://www.gromacs.org/pipermail/gmx-users/2005-December/018997.html but it doesn't seem like it was resolved. Is there an easy way to do this (aside from going into the .gro file and manually deleting the unwanted waters!) genbox 3.3.1 has an option to set the maximum number of waters. Thanks, Arneh ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Genbox - Removal of Unwanted Waters
Arneh Babakhani wrote: Thanks for the input. Is there a way to restrict the water from a certain space (in other words, to confine it a certain location)? just the shell option, otherwise no. genbox -h Thanks, Arneh David van der Spoel wrote: Arneh Babakhani wrote: Hello all, How do you remove unwanted waters (or how do you prevent genbox from placing unwanted waters) after you solvate by genbox? This problem was posted once before, http://www.gromacs.org/pipermail/gmx-users/2005-December/018997.html but it doesn't seem like it was resolved. Is there an easy way to do this (aside from going into the .gro file and manually deleting the unwanted waters!) genbox 3.3.1 has an option to set the maximum number of waters. Thanks, Arneh ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Genbox - Removal of Unwanted Waters
Great, thank you very much, will try it out,
[EMAIL PROTECTED] wrote:
If I have a solvated membrane and I want to extend the z dimension and add new
waters there, this is what I do. The script could be modified to get rid of new
waters in any x/y/z dimensions (around line 41 of the script).
1. run genbox on initial.gro to create solvated.gro
2. cp solvated.gro new_waters.gro
3. use vi to remove everything in new_waters.gro except the new waters (make
sure you remove waters that were in initial.gro)
4. use vi to edit keepbyz.pl
- upperz and lowerz variables as you please
- sol to the name of your solvent molecule
5. run keepbyz.pl on new_waters.gro
./keepbyz new_waters.gro keep_these_waters.gro
6. tail -1 initial.gro last_line.gro
7. head -$(expr $(cat initial.gro | wc -l | awk '{print $1}') - 1 ) initial.gro
not_last_line.gro
8. cat not_last_line.gro new_waters.gro last_line.gro new_system.gro
9. editconf -f new_system.gro -o new_system_sequential_numbers.gro
Here is the script (make sure you chmod +x keepbyz.pl):
#!/bin/bash
# give x.gro as first command line arguement
upperz=6.417
lowerz=0.820
sol=SOL
count=0
cat $1 | grep $sol | while read line; do
for first in $line; do
break
done
if [ $count = 3 ]; then
count=0
fi
count=$(expr $count + 1)
if [ $count != 1 ]; then
continue
fi
l=${#line}
m=$(expr $l - 24)
i=1
for word in ${line:$m}; do
if [ $i = 1 ]; then
popex=$word
else
if [ $i = 2 ]; then
popey=$word
else
if [ $i = 3 ]; then
popez=$word
break
fi
fi
fi
i=$(expr $i + 1)
done
nolx=`echo $popez $upperz | bc`
nohx=`echo $popez $lowerz | bc`
myno=$(expr $nolx + $nohx)
if [ $myno != 0 ]; then
z=${#first}
if [ $z != 8 ]; then
sfirst=[[:space:]]$first
else
sfirst=$first
fi
`echo grep $sfirst $1`
fi
done
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Re: [gmx-users] genbox overlap checking
hi roman, On Thu, 2006-03-09 at 17:14 +0100, Roman Holomb wrote: Dear all, I have problem with using genbox When I try to add more than 20 BF4 molecules in the box (3.2 3.2 3.2) by genbox -ci BF4_1.gro -nmol 20 -box 3.2 -o BF4_20.gro probably you need to indicate a bigger van der waals distance by -vdwd for your insert. as an alternative, why don't you stack your molecule with genconf? then each molecule has as much space as in the unit box. regards, daniela I usualy have connected BF4 molecules. Changes in the vdwradii.dat file not help. Also during adding molecules I can see something like: - Going to determine what solvent types we have. There are 0 molecules, 5 charge groups and 5 atoms There are 0 optimized solvent molecules on node 0 There are 0 optimized water molecules on node 0 Grid: 4 x 4 x 4 cells nri = 7, nrj = 10 Checking Protein-Solvent overlap: tested 0 pairs, removed 0 atoms. Checking Solvent-Solvent overlap: tested 0 pairs, removed 0 atoms. Try 1box_margin = 1.56! Removed 0 atoms that were outside the box nri = 7, nrj = 10 Checking Protein-Solvent overlap: tested 0 pairs, removed 0 atoms. Checking Solvent-Solvent overlap: tested 0 pairs, removed 0 atoms. Try 2box_margin = 1.56)! - So ... overlap testing seem not work but why??? Any suggestion? Sincerely Roman -- Daniela S. Mueller biologist (Diplom, German degree) __ - Molecular Dynamics Group, UQ - Address: School of Molecular and Microbial Sciences (SMMS) Chemistry Building (#68) University of Queensland Qld 4072, Brisbane Australia Phone: +61-7-33653732 Website: http://ilc00f.facbacs.uq.edu.au/SMMS/a_mark/Front.htm ** - MD group, RuG - Address: Molecular Dynamics Dept. of Biophysical Chemistry University of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands Website: http://www.rug.nl/gbb/md __ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] genbox problem
Roman Holomb wrote: Dear Gromacs users, I use genbox for random insert 100 BF4 molecules in the box. But there are so many connections between BF4 anions . I have decreased number of molecules to 20 but I have the same problem. Sometimes this can be fixed by energy minimization. After optimization I have no connections between different BF4 anions but there are small amount of BF4 with F-F bonds. This is realy problem to use genbox for generate the model (I plan to make more complicated systems and I have no posibility to correct models by hand So my question is: Can I do something with parameters (VDW coulomb distance) to get correct results from genbox? Seems nothing influence here . edit vdwradii.dat Thanks Sincerely /Roman ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
