my script is #!/bin/bash
trjconv -s 10nsnvt.tpr -f 10nsnvt.trr -o noPBC.xtc -pbc none -ur compact -center -n index.ndx << EOF 2 0 EOF trjconv -s 10nsnvt.tpr -f noPBC.xtc -o fit.xtc -fit rot+trans -n index.ndx << EOF 2 0 EOF g_spatial -f fit.xtc -s 10nsnvt.tpr -n index.ndx << EOF 6 7 EOF g_spatial -f fit.xtc -s 10nsnvt.tpr -n index.ndx << EOF 2 2 EOF ............................................................................................. after script 2 grid.cube files imported in VMD .......................................................................................... [srinivas@cclw1 g_ac-life]$ ./run.sh :-) G R O M A C S (-: Great Red Oystrich Makes All Chemists Sane :-) VERSION 4.6.3 (-: Contributions from Mark Abraham, Emile Apol, Rossen Apostolov, Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Christoph Junghans, Peter Kasson, Carsten Kutzner, Per Larsson, Pieter Meulenhoff, Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz, Michael Shirts, Alfons Sijbers, Peter Tieleman, Berk Hess, David van der Spoel, and Erik Lindahl. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2012,2013, The GROMACS development team at Uppsala University & The Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information. This program is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. :-) trjconv (-: Option Filename Type Description ------------------------------------------------------------ -f 10nsnvt.trr Input Trajectory: xtc trr trj gro g96 pdb cpt -o noPBC.xtc Output Trajectory: xtc trr trj gro g96 pdb -s 10nsnvt.tpr Input, Opt! Structure+mass(db): tpr tpb tpa gro g96 pdb -n index.ndx Input, Opt! Index file -fr frames.ndx Input, Opt. Index file -sub cluster.ndx Input, Opt. Index file -drop drop.xvg Input, Opt. xvgr/xmgr file Option Type Value Description ------------------------------------------------------ -[no]h bool no Print help info and quit -[no]version bool no Print version info and quit -nice int 19 Set the nicelevel -b time 0 First frame (ps) to read from trajectory -e time 0 Last frame (ps) to read from trajectory -tu enum ps Time unit: fs, ps, ns, us, ms or s -[no]w bool no View output .xvg, .xpm, .eps and .pdb files -xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none -skip int 1 Only write every nr-th frame -dt time 0 Only write frame when t MOD dt = first time (ps) -[no]round bool no Round measurements to nearest picosecond -dump time -1 Dump frame nearest specified time (ps) -t0 time 0 Starting time (ps) (default: don't change) -timestep time 0 Change time step between input frames (ps) -pbc enum none PBC treatment (see help text for full description): none, mol, res, atom, nojump, cluster or whole -ur enum compact Unit-cell representation: rect, tric or compact -[no]center bool yes Center atoms in box -boxcenter enum tric Center for -pbc and -center: tric, rect or zero -box vector 0 0 0 Size for new cubic box (default: read from input) -clustercenter vector 0 0 0 Optional starting point for pbc cluster option -trans vector 0 0 0 All coordinates will be translated by trans. This can advantageously be combined with -pbc mol -ur compact. -shift vector 0 0 0 All coordinates will be shifted by framenr*shift -fit enum none Fit molecule to ref structure in the structure file: none, rot+trans, rotxy+transxy, translation, transxy or progressive -ndec int 3 Precision for .xtc and .gro writing in number of decimal places -[no]vel bool yes Read and write velocities if possible -[no]force bool no Read and write forces if possible -trunc time -1 Truncate input trajectory file after this time (ps) -exec string Execute command for every output frame with the frame number as argument -[no]app bool no Append output -split time 0 Start writing new file when t MOD split = first time (ps) -[no]sep bool no Write each frame to a separate .gro, .g96 or .pdb file -nzero int 0 If the -sep flag is set, use these many digits for the file numbers and prepend zeros as needed -dropunder real 0 Drop all frames below this value -dropover real 0 Drop all frames above this value -[no]conect bool no Add conect records when writing .pdb files. Useful for visualization of non-standard molecules, e.g. coarse grained ones WARNING: Option for unitcell representation (-ur compact) only has effect in combination with -pbc mol, res or atom. Ingoring unitcell representation. Will write xtc: Compressed trajectory (portable xdr format) Reading file 10nsnvt.tpr, VERSION 4.6.3 (single precision) Reading file 10nsnvt.tpr, VERSION 4.6.3 (single precision) Select group for centering Group 0 ( System) has 11985 elements Group 1 ( Other) has 36 elements Group 2 ( _MMO) has 36 elements Group 3 ( Water) has 11949 elements Group 4 ( SOL) has 11949 elements Group 5 ( non-Water) has 36 elements Group 6 ( H8M_HAU_H8N) has 3 elements Group 7 ( OW) has 3983 elements Select a group: Selected 2: '_MMO' Select group for output Group 0 ( System) has 11985 elements Group 1 ( Other) has 36 elements Group 2 ( _MMO) has 36 elements Group 3 ( Water) has 11949 elements Group 4 ( SOL) has 11949 elements Group 5 ( non-Water) has 36 elements Group 6 ( H8M_HAU_H8N) has 3 elements Group 7 ( OW) has 3983 elements Select a group: Selected 0: 'System' trn version: GMX_trn_file (single precision) Reading frame 0 time 0.000 Setting output precision to 0.001 (nm) Back Off! I just backed up noPBC.xtc to ./#noPBC.xtc.19# Last frame 10000 time 10000.000 -> frame 10000 time 10000.000 gcq#167: "The Poodle Bites" (F. Zappa) :-) G R O M A C S (-: S C A M O R G :-) VERSION 4.6.3 (-: Contributions from Mark Abraham, Emile Apol, Rossen Apostolov, Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Christoph Junghans, Peter Kasson, Carsten Kutzner, Per Larsson, Pieter Meulenhoff, Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz, Michael Shirts, Alfons Sijbers, Peter Tieleman, Berk Hess, David van der Spoel, and Erik Lindahl. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2012,2013, The GROMACS development team at Uppsala University & The Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information. This program is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. :-) trjconv (-: Option Filename Type Description ------------------------------------------------------------ -f noPBC.xtc Input Trajectory: xtc trr trj gro g96 pdb cpt -o fit.xtc Output Trajectory: xtc trr trj gro g96 pdb -s 10nsnvt.tpr Input, Opt! Structure+mass(db): tpr tpb tpa gro g96 pdb -n index.ndx Input, Opt! Index file -fr frames.ndx Input, Opt. Index file -sub cluster.ndx Input, Opt. Index file -drop drop.xvg Input, Opt. xvgr/xmgr file Option Type Value Description ------------------------------------------------------ -[no]h bool no Print help info and quit -[no]version bool no Print version info and quit -nice int 19 Set the nicelevel -b time 0 First frame (ps) to read from trajectory -e time 0 Last frame (ps) to read from trajectory -tu enum ps Time unit: fs, ps, ns, us, ms or s -[no]w bool no View output .xvg, .xpm, .eps and .pdb files -xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none -skip int 1 Only write every nr-th frame -dt time 0 Only write frame when t MOD dt = first time (ps) -[no]round bool no Round measurements to nearest picosecond -dump time -1 Dump frame nearest specified time (ps) -t0 time 0 Starting time (ps) (default: don't change) -timestep time 0 Change time step between input frames (ps) -pbc enum none PBC treatment (see help text for full description): none, mol, res, atom, nojump, cluster or whole -ur enum rect Unit-cell representation: rect, tric or compact -[no]center bool no Center atoms in box -boxcenter enum tric Center for -pbc and -center: tric, rect or zero -box vector 0 0 0 Size for new cubic box (default: read from input) -clustercenter vector 0 0 0 Optional starting point for pbc cluster option -trans vector 0 0 0 All coordinates will be translated by trans. This can advantageously be combined with -pbc mol -ur compact. -shift vector 0 0 0 All coordinates will be shifted by framenr*shift -fit enum rot+trans Fit molecule to ref structure in the structure file: none, rot+trans, rotxy+transxy, translation, transxy or progressive -ndec int 3 Precision for .xtc and .gro writing in number of decimal places -[no]vel bool yes Read and write velocities if possible -[no]force bool no Read and write forces if possible -trunc time -1 Truncate input trajectory file after this time (ps) -exec string Execute command for every output frame with the frame number as argument -[no]app bool no Append output -split time 0 Start writing new file when t MOD split = first time (ps) -[no]sep bool no Write each frame to a separate .gro, .g96 or .pdb file -nzero int 0 If the -sep flag is set, use these many digits for the file numbers and prepend zeros as needed -dropunder real 0 Drop all frames below this value -dropover real 0 Drop all frames above this value -[no]conect bool no Add conect records when writing .pdb files. Useful for visualization of non-standard molecules, e.g. coarse grained ones Will write xtc: Compressed trajectory (portable xdr format) Reading file 10nsnvt.tpr, VERSION 4.6.3 (single precision) Reading file 10nsnvt.tpr, VERSION 4.6.3 (single precision) Select group for least squares fit Group 0 ( System) has 11985 elements Group 1 ( Other) has 36 elements Group 2 ( _MMO) has 36 elements Group 3 ( Water) has 11949 elements Group 4 ( SOL) has 11949 elements Group 5 ( non-Water) has 36 elements Group 6 ( H8M_HAU_H8N) has 3 elements Group 7 ( OW) has 3983 elements Select a group: Selected 2: '_MMO' Select group for output Group 0 ( System) has 11985 elements Group 1 ( Other) has 36 elements Group 2 ( _MMO) has 36 elements Group 3 ( Water) has 11949 elements Group 4 ( SOL) has 11949 elements Group 5 ( non-Water) has 36 elements Group 6 ( H8M_HAU_H8N) has 3 elements Group 7 ( OW) has 3983 elements Select a group: Selected 0: 'System' Reading frame 0 time 0.000 Precision of noPBC.xtc is 0.001 (nm) Using output precision of 0.001 (nm) Back Off! I just backed up fit.xtc to ./#fit.xtc.22# Last frame 10000 time 10000.000 -> frame 10000 time 10000.000 gcq#1: "I Live the Life They Wish They Did" (Tricky) :-) G R O M A C S (-: Good gRace! Old Maple Actually Chews Slate :-) VERSION 4.6.3 (-: Contributions from Mark Abraham, Emile Apol, Rossen Apostolov, Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Christoph Junghans, Peter Kasson, Carsten Kutzner, Per Larsson, Pieter Meulenhoff, Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz, Michael Shirts, Alfons Sijbers, Peter Tieleman, Berk Hess, David van der Spoel, and Erik Lindahl. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2012,2013, The GROMACS development team at Uppsala University & The Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information. This program is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. :-) g_spatial (-: Option Filename Type Description ------------------------------------------------------------ -s 10nsnvt.tpr Input Structure+mass(db): tpr tpb tpa gro g96 pdb -f fit.xtc Input Trajectory: xtc trr trj gro g96 pdb cpt -n index.ndx Input, Opt! Index file Option Type Value Description ------------------------------------------------------ -[no]h bool no Print help info and quit -[no]version bool no Print version info and quit -nice int 0 Set the nicelevel -b time 0 First frame (ps) to read from trajectory -e time 0 Last frame (ps) to read from trajectory -dt time 0 Only use frame when t MOD dt = first time (ps) -[no]w bool no View output .xvg, .xpm, .eps and .pdb files -[no]pbc bool no Use periodic boundary conditions for computing distances -[no]div bool yes Calculate and apply the divisor for bin occupancies based on atoms/minimal cube size. Set as TRUE for visualization and as FALSE (-nodiv) to get accurate counts per frame -ign int -1 Do not display this number of outer cubes (positive values may reduce boundary speckles; -1 ensures outer surface is visible) -bin real 0.05 Width of the bins (nm) -nab int 4 Number of additional bins to ensure proper memory allocation Reading file 10nsnvt.tpr, VERSION 4.6.3 (single precision) Reading file 10nsnvt.tpr, VERSION 4.6.3 (single precision) Select group to generate SDF: Group 0 ( System) has 11985 elements Group 1 ( Other) has 36 elements Group 2 ( _MMO) has 36 elements Group 3 ( Water) has 11949 elements Group 4 ( SOL) has 11949 elements Group 5 ( non-Water) has 36 elements Group 6 ( H8M_HAU_H8N) has 3 elements Group 7 ( OW) has 3983 elements Select a group: Selected 6: 'H8M_HAU_H8N' Select group to output coords (e.g. solute): Group 0 ( System) has 11985 elements Group 1 ( Other) has 36 elements Group 2 ( _MMO) has 36 elements Group 3 ( Water) has 11949 elements Group 4 ( SOL) has 11949 elements Group 5 ( non-Water) has 36 elements Group 6 ( H8M_HAU_H8N) has 3 elements Group 7 ( OW) has 3983 elements Select a group: Selected 7: 'OW' Last frame 10000 time 10000.000 Back Off! I just backed up grid.cube to ./#grid.cube.12# Counts per frame in all 3168 cubes divided by 9.469697e-04 Normalized data: average 1.000000e+00, min 0.000000e+00, max 7.855854e+01 gcq#52: "You Think That You're Bigger When You Fill the Void" (Urban Dance Squad) [srinivas@cclw1 g_ac-life]$ g_spatial -f fit.xtc -s 10nsnvt.tpr -n index.ndx :-) G R O M A C S (-: Gromacs Runs One Microsecond At Cannonball Speeds :-) VERSION 4.6.3 (-: Contributions from Mark Abraham, Emile Apol, Rossen Apostolov, Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Christoph Junghans, Peter Kasson, Carsten Kutzner, Per Larsson, Pieter Meulenhoff, Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz, Michael Shirts, Alfons Sijbers, Peter Tieleman, Berk Hess, David van der Spoel, and Erik Lindahl. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2012,2013, The GROMACS development team at Uppsala University & The Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information. This program is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. :-) g_spatial (-: Option Filename Type Description ------------------------------------------------------------ -s 10nsnvt.tpr Input Structure+mass(db): tpr tpb tpa gro g96 pdb -f fit.xtc Input Trajectory: xtc trr trj gro g96 pdb cpt -n index.ndx Input, Opt! Index file Option Type Value Description ------------------------------------------------------ -[no]h bool no Print help info and quit -[no]version bool no Print version info and quit -nice int 0 Set the nicelevel -b time 0 First frame (ps) to read from trajectory -e time 0 Last frame (ps) to read from trajectory -dt time 0 Only use frame when t MOD dt = first time (ps) -[no]w bool no View output .xvg, .xpm, .eps and .pdb files -[no]pbc bool no Use periodic boundary conditions for computing distances -[no]div bool yes Calculate and apply the divisor for bin occupancies based on atoms/minimal cube size. Set as TRUE for visualization and as FALSE (-nodiv) to get accurate counts per frame -ign int -1 Do not display this number of outer cubes (positive values may reduce boundary speckles; -1 ensures outer surface is visible) -bin real 0.05 Width of the bins (nm) -nab int 4 Number of additional bins to ensure proper memory allocation Reading file 10nsnvt.tpr, VERSION 4.6.3 (single precision) Reading file 10nsnvt.tpr, VERSION 4.6.3 (single precision) Select group to generate SDF: Group 0 ( System) has 11985 elements Group 1 ( Other) has 36 elements Group 2 ( _MMO) has 36 elements Group 3 ( Water) has 11949 elements Group 4 ( SOL) has 11949 elements Group 5 ( non-Water) has 36 elements Group 6 ( H8M_HAU_H8N) has 3 elements Group 7 ( OW) has 3983 elements Select a group: 2 Selected 2: '_MMO' Select group to output coords (e.g. solute): Group 0 ( System) has 11985 elements Group 1 ( Other) has 36 elements Group 2 ( _MMO) has 36 elements Group 3 ( Water) has 11949 elements Group 4 ( SOL) has 11949 elements Group 5 ( non-Water) has 36 elements Group 6 ( H8M_HAU_H8N) has 3 elements Group 7 ( OW) has 3983 elements Select a group: 2 Selected 2: '_MMO' Last frame 10000 time 10000.000 Counts per frame in all 13224 cubes divided by 2.722323e-03 Normalized data: average 1.000000e+00, min 0.000000e+00, max 1.652467e+02 gcq#213: "Engage" (J.L. Picard) [srinivas@cclw1 g_ac-life]$ vmd grid.cube ...................................................................................... molecule and SDF surface are overlapping somewhat . why? is this wrong result???? ....................................................................................... Thank you very much for your kind reply sir <http://gromacs.5086.x6.nabble.com/file/n5013546/OH.jpeg> -- View this message in context: http://gromacs.5086.x6.nabble.com/g-spatial-merging-solvent-ond-solute-need-some-distance-tp5013538p5013546.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.