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  11 <td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_hbond</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_hbond computes and analyzes hydrogen bonds. Hydrogen bonds are
  18 determined based on cutoffs for the angle Acceptor - Donor - Hydrogen
  19 (zero is extended) and the distance Hydrogen - Acceptor.
  20 OH and NH groups are regarded as donors, O is an acceptor always,
  21 N is an acceptor by default, but this can be switched using
  22 <tt>-nitacc</tt>. Dummy hydrogen atoms are assumed to be connected
  23 to the first preceding non-hydrogen atom.<p>
  24 You need to specify two groups for analysis, which must be either
  25 identical or non-overlapping. All hydrogen bonds between the two
  26 groups are analyzed.<p>
  27 If you set -shell, you will be asked for an additional index group
  28 which should contain exactly one atom. In this case, only hydrogen
  29 bonds between atoms within the shell distance from the one atom are
  30 considered.<p>
  31 <tt>
  32 [ selected ]<br>
  33      20    21    24<br>
  34      25    26    29<br>
  35       1     3     6<br>
  36 </tt><br>
  37 Note that the triplets need not be on separate lines.
  38 Each atom triplet specifies a hydrogen bond to be analyzed,
  39 note also that no check is made for the types of atoms.<p>
  40 <b>Output:</b><br>
  41 <tt>-num</tt>:  number of hydrogen bonds as a function of time.<br>
  42 <tt>-ac</tt>:   average over all autocorrelations of the existence
  43 functions (either 0 or 1) of all hydrogen bonds.<br>
  44 <tt>-dist</tt>: distance distribution of all hydrogen bonds.<br>
  45 <tt>-ang</tt>:  angle distribution of all hydrogen bonds.<br>
  46 <tt>-hx</tt>:   the number of n-n+i hydrogen bonds as a function of time
  47 where n and n+i stand for residue numbers and i ranges from 0 to 6.
  48 This includes the n-n+3, n-n+4 and n-n+5 hydrogen bonds associated
  49 with helices in proteins.<br>
  50 <tt>-hbn</tt>:  all selected groups, donors, hydrogens and acceptors
  51 for selected groups, all hydrogen bonded atoms from all groups and
  52 all solvent atoms involved in insertion.<br>
  53 <tt>-hbm</tt>:  existence matrix for all hydrogen bonds over all
  54 frames, this also contains information on solvent insertion
  55 into hydrogen bonds. Ordering is identical to that in <tt>-hbn</tt>
  56 index file.<br>
  57 <tt>-dan</tt>: write out the number of donors and acceptors analyzed for
  58 each timeframe. This is especially useful when using <tt>-shell</tt>.<br>
  59 <tt>-nhbdist</tt>: compute the number of HBonds per hydrogen in order to
  60 compare results to Raman Spectroscopy.
  61 <p>
  62 Note: options <tt>-ac</tt>, <tt>-life</tt>, <tt>-hbn</tt> and <tt>-hbm</tt>
  63 require an amount of memory proportional to the total numbers of donors
  64 times the total number of acceptors in the selected group(s).
  65 <P>
  66 <H3>Files</H3>
  67 <TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
  68 <TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
  69 <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>
  70 <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> Run input file: <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> </TD></TR>
  71 <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>
  72 <TR><TD ALIGN=RIGHT> <b><tt>-num</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">   hbnum.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
  73 <TR><TD ALIGN=RIGHT> <b><tt>-g</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="log.html">   hbond.log</a></tt> </TD><TD> Output, Opt. </TD><TD> Log file </TD></TR>
  74 <TR><TD ALIGN=RIGHT> <b><tt>-ac</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">    hbac.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
  75 <TR><TD ALIGN=RIGHT> <b><tt>-dist</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">  hbdist.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
  76 <TR><TD ALIGN=RIGHT> <b><tt>-ang</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">   hbang.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
  77 <TR><TD ALIGN=RIGHT> <b><tt>-hx</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> hbhelix.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
  78 <TR><TD ALIGN=RIGHT> <b><tt>-hbn</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html">   hbond.ndx</a></tt> </TD><TD> Output, Opt. </TD><TD> Index file </TD></TR>
  79 <TR><TD ALIGN=RIGHT> <b><tt>-hbm</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xpm.html">   hbmap.xpm</a></tt> </TD><TD> Output, Opt. </TD><TD> X PixMap compatible matrix file </TD></TR>
  80 <TR><TD ALIGN=RIGHT> <b><tt>-don</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">   donor.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
  81 <TR><TD ALIGN=RIGHT> <b><tt>-dan</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">   danum.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
  82 <TR><TD ALIGN=RIGHT> <b><tt>-life</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">  hblife.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
  83 <TR><TD ALIGN=RIGHT> <b><tt>-nhbdist</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> nhbdist.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
  84 </TABLE>
  85 <P>
  86 <H3>Other options</H3>
  87 <TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
  88 <TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
  89 <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>
  90 <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>
  91 <TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
  92 <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>
  93 <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>
  94 <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>
  95 <TR><TD ALIGN=RIGHT> <b><tt>-xvg</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>xmgrace</tt> </TD><TD> <a href="xvg.html">xvg</a> plot formatting: <tt>xmgrace</tt>, <tt>xmgr</tt> or <tt>none</tt> </TD></TD>
  96 <TR><TD ALIGN=RIGHT> <b><tt>-a</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>30    </tt> </TD><TD> Cutoff angle (degrees, Acceptor - Donor - Hydrogen) </TD></TD>
  97 <TR><TD ALIGN=RIGHT> <b><tt>-r</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0.35  </tt> </TD><TD> Cutoff radius (nm, X - Acceptor, see next option) </TD></TD>
  98 <TR><TD ALIGN=RIGHT> <b><tt>-[no]da</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>yes   </tt> </TD><TD> Use distance Donor-Acceptor (if TRUE) or Hydrogen-Acceptor (FALSE) </TD></TD>
  99 <TR><TD ALIGN=RIGHT> <b><tt>-r2</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0     </tt> </TD><TD> Second cutoff radius. Mainly useful with -contact and -ac </TD></TD>
 100 <TR><TD ALIGN=RIGHT> <b><tt>-abin</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>1     </tt> </TD><TD> Binwidth angle distribution (degrees) </TD></TD>
 101 <TR><TD ALIGN=RIGHT> <b><tt>-rbin</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0.005 </tt> </TD><TD> Binwidth distance distribution (nm) </TD></TD>
 102 <TR><TD ALIGN=RIGHT> <b><tt>-[no]nitacc</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>yes   </tt> </TD><TD> Regard nitrogen atoms as acceptors </TD></TD>
 103 <TR><TD ALIGN=RIGHT> <b><tt>-[no]contact</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Do not look for hydrogen bonds, but merely for contacts within the cut-off distance </TD></TD>
 104 <TR><TD ALIGN=RIGHT> <b><tt>-shell</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>-1    </tt> </TD><TD> when &gt; 0, only calculate hydrogen bonds within # nm shell around one particle </TD></TD>
 105 <TR><TD ALIGN=RIGHT> <b><tt>-fitstart</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>1     </tt> </TD><TD> Time (ps) from which to start fitting the correlation functions in order to obtain the forward and backward rate constants for HB breaking and formation. With -gemfit we suggest -fitstart 0 </TD></TD>
 106 <TR><TD ALIGN=RIGHT> <b><tt>-fitstart</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>1     </tt> </TD><TD> Time (ps) to which to stop fitting the correlation functions in order to obtain the forward and backward rate constants for HB breaking and formation (only with -gemfit) </TD></TD>
 107 <TR><TD ALIGN=RIGHT> <b><tt>-temp</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>298.15</tt> </TD><TD> Temperature (K) for computing the Gibbs energy corresponding to HB breaking and reforming </TD></TD>
 108 <TR><TD ALIGN=RIGHT> <b><tt>-smooth</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>-1    </tt> </TD><TD> If &gt;= 0, the tail of the ACF will be smoothed by fitting it to an exponential function: y = A exp(-x/tau) </TD></TD>
 109 <TR><TD ALIGN=RIGHT> <b><tt>-dump</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Dump the first N hydrogen bond ACFs in a single <a href="xvg.html">xvg</a> file for debugging </TD></TD>
 110 <TR><TD ALIGN=RIGHT> <b><tt>-max_hb</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0     </tt> </TD><TD> Theoretical maximum number of hydrogen bonds used for normalizing HB autocorrelation function. Can be useful in case the program estimates it wrongly </TD></TD>
 111 <TR><TD ALIGN=RIGHT> <b><tt>-[no]merge</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>yes   </tt> </TD><TD> H-bonds between the same donor and acceptor, but with different hydrogen are treated as a single H-bond. Mainly important for the ACF. </TD></TD>
 112 <TR><TD ALIGN=RIGHT> <b><tt>-geminate</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>none</tt> </TD><TD> Use reversible geminate recombination for the kinetics/thermodynamics calclations. See Markovitch et al., J. Chem. Phys 129, 084505 (2008) for details.: <tt>none</tt>, <tt>dd</tt>, <tt>ad</tt>, <tt>aa</tt> or <tt>a4</tt> </TD></TD>
 113 <TR><TD ALIGN=RIGHT> <b><tt>-diff</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>-1    </tt> </TD><TD> Dffusion coefficient to use in the rev. gem. recomb. kinetic model. If non-positive, then it will be fitted to the ACF along with ka and kd. </TD></TD>
 114 <TR><TD ALIGN=RIGHT> <b><tt>-acflen</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>-1</tt> </TD><TD> Length of the ACF, default is half the number of frames </TD></TD>
 115 <TR><TD ALIGN=RIGHT> <b><tt>-[no]normalize</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>yes   </tt> </TD><TD> Normalize ACF </TD></TD>
 116 <TR><TD ALIGN=RIGHT> <b><tt>-P</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Order of Legendre polynomial for ACF (0 indicates none): <tt>0</tt>, <tt>1</tt>, <tt>2</tt> or <tt>3</tt> </TD></TD>
 117 <TR><TD ALIGN=RIGHT> <b><tt>-fitfn</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>none</tt> </TD><TD> Fit function: <tt>none</tt>, <tt>exp</tt>, <tt>aexp</tt>, <tt>exp_exp</tt>, <tt>vac</tt>, <tt>exp5</tt>, <tt>exp7</tt> or <tt>exp9</tt> </TD></TD>
 118 <TR><TD ALIGN=RIGHT> <b><tt>-ncskip</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Skip N points in the output file of correlation functions </TD></TD>
 119 <TR><TD ALIGN=RIGHT> <b><tt>-beginfit</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0     </tt> </TD><TD> Time where to begin the exponential fit of the correlation function </TD></TD>
 120 <TR><TD ALIGN=RIGHT> <b><tt>-endfit</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>-1    </tt> </TD><TD> Time where to end the exponential fit of the correlation function, -1 is until the end </TD></TD>
 121 </TABLE>
 122 <P>
 123 <H3>Known problems</H3>
 124 <UL>
 125 <LI>The option <tt>-sel</tt> that used to work on selected hbonds is out of order, and therefore not available for the time being.
 126 </UL>
 127 <P>
 128 <hr>
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 130 <font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
 131 <font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
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