[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
<http://gromacs.5086.x6.nabble.com/file/n5013546/OH.jpeg>

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