[gmx-users] genbox -nmol, atoms removed
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? Thanks, Xu Dong Huang Chemical Biochemical Engineering Rutgers School of Engineering xudo...@eden.rutgers.edu -- 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
