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  10 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
  11 <td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_spatial</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
  12 </TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.5<br>
  13 Thu 26 Aug 2010</B></td></tr></TABLE>
  14 <HR>
  15 <H3>Description</H3>
  16 <p>
  17 g_spatial calculates the spatial distribution function and
  18 outputs it in a form that can be read by VMD as Gaussian98 cube format.
  19 This was developed from template.c (gromacs-3.3).
  20 For a system of 32K atoms and a 50ns trajectory, the SDF can be generated
  21 in about 30 minutes, with most of the time dedicated to the two runs through
  22 <a href="trjconv.html">trjconv</a> that are required to center everything properly.
  23 This also takes a whole bunch of space (3 copies of the <a href="xtc.html">xtc</a> file).
  24 Still, the pictures are pretty and very informative when the fitted selection is properly made.
  25 3-4 atoms in a widely mobile group like a free amino acid in solution works
  26 well, or select the protein backbone in a stable folded structure to get the SDF
  27 of solvent and look at the time-averaged solvation shell.
  28 It is also possible using this program to generate the SDF based on some arbitrarty
  29 Cartesian coordinate. To do that, simply omit the preliminary <a href="trjconv.html">trjconv</a> steps.
  30
  31 USAGE:
  32
  33 1. Use <a href="make_<a href="ndx.html">ndx</a>.html">make_<a href="ndx.html">ndx</a></a> to create a group containing the atoms around which you want the SDF
  34
  35 2. <a href="trjconv.html">trjconv</a> -s a.<a href="tpr.html">tpr</a> -f a.<a href="xtc.html">xtc</a> -o b.<a href="xtc.html">xtc</a> -center tric -ur compact -pbc none
  36
  37 3. <a href="trjconv.html">trjconv</a> -s a.<a href="tpr.html">tpr</a> -f b.<a href="xtc.html">xtc</a> -o c.<a href="xtc.html">xtc</a> -fit rot+trans
  38
  39 4. run g_spatial on the <a href="xtc.html">xtc</a> output of step #3.
  40
  41 5. Load grid.cube into VMD and view as an isosurface.
  42
  43 *** Systems such as micelles will require <a href="trjconv.html">trjconv</a> -pbc cluster between steps 1 and 2
  44
  45 WARNINGS:
  46
  47 The SDF will be generated for a cube that contains all bins that have some non-zero occupancy.
  48 However, the preparatory -fit rot+trans option to <a href="trjconv.html">trjconv</a> implies that your system will be rotating
  49 and translating in space (in order that the selected group does not). Therefore the values that are
  50 returned will only be valid for some region around your central group/coordinate that has full overlap
  51 with system volume throughout the entire translated/rotated system over the course of the trajectory.
  52 It is up to the user to ensure that this is the case.
  53
  54 BUGS:
  55
  56 When the allocated memory is not large enough, a segmentation fault may occur. This is usually detected
  57 and the program is halted prior to the fault while displaying a warning message suggesting the use of the -nab
  58 option. However, the program does not detect all such events. If you encounter a segmentation fault, run it again
  59 with an increased -nab value.
  60
  61 RISKY OPTIONS:
  62
  63 To reduce the amount of space and time required, you can output only the coords
  64 that are going to be used in the first and subsequent run through <a href="trjconv.html">trjconv</a>.
  65 However, be sure to set the -nab option to a sufficiently high value since
  66 memory is allocated for cube bins based on the initial coords and the -nab
  67 (Number of Additional Bins) option value.
  68
  69 <P>
  70 <H3>Files</H3>
  71 <TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
  72 <TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
  73 <TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html">   topol.tpr</a></tt> </TD><TD> Input </TD><TD> Structure+mass(db): <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
  74 <TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html">    traj.xtc</a></tt> </TD><TD> Input </TD><TD> Trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> cpt </TD></TR>
  75 <TR><TD ALIGN=RIGHT> <b><tt>-n</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html">   index.ndx</a></tt> </TD><TD> Input, Opt. </TD><TD> Index file </TD></TR>
  76 </TABLE>
  77 <P>
  78 <H3>Other options</H3>
  79 <TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
  80 <TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
  81 <TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Print help info and quit </TD></TD>
  82 <TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Print version info and quit </TD></TD>
  83 <TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Set the nicelevel </TD></TD>
  84 <TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0     </tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
  85 <TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0     </tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
  86 <TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0     </tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
  87 <TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
  88 <TR><TD ALIGN=RIGHT> <b><tt>-[no]pbc</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Use periodic boundary conditions for computing distances </TD></TD>
  89 <TR><TD ALIGN=RIGHT> <b><tt>-[no]div</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>yes   </tt> </TD><TD> 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 </TD></TD>
  90 <TR><TD ALIGN=RIGHT> <b><tt>-ign</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>-1</tt> </TD><TD> Do not display this number of outer cubes (positive values may reduce boundary speckles; -1 ensures outer surface is visible) </TD></TD>
  91 <TR><TD ALIGN=RIGHT> <b><tt>-bin</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0.05  </tt> </TD><TD> Width of the bins in nm </TD></TD>
  92 <TR><TD ALIGN=RIGHT> <b><tt>-nab</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>4</tt> </TD><TD> Number of additional bins to ensure proper memory allocation </TD></TD>
  93 </TABLE>
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