[gmx-users] g_spatial: merging solvent ond solute:::need some distance
Christopher Neale
chris.neale at alum.utoronto.ca
Sun Dec 29 04:27:59 CET 2013
Perhaps your central molecule is flexible? Then it makes sense that a single frame of your solute can sometimes overlap with the time and ensemble averaged spatial density of the solvent. Nevertheless, your image looked strange since the solvent (I presume it is the SDF of the solvent) is only on one side of the solute (I presume that you fit on the solute).
You can test that theory by loading in the fit.xtc trajectory into VMD, then create a representation to show the solute only, and then on the trajectory tab put 0:10:100 or something like that (see VMD for more info, but it is start:stride:end). Then do the same for your solute group. You will then see that these two crude representations of average densities may overlap.
Still, since your SDF looked strange to me (density only on one side), maybe you can describe what each group is (not just .ndx codes please) and what you are trying to do.
Chris.
________________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of srinivasa rao lanke <srinu1982 at hotmail.com>
Sent: 27 December 2013 00:38
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] g_spatial: merging solvent ond solute:::need some distance
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 at 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 at 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 at 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
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