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  11 <td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_tune_pme</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 For a given number <tt>-np</tt> or <tt>-nt</tt> of processors/threads, this program systematically
  18 times <a href="mdrun.html">mdrun</a> with various numbers of PME-only nodes and determines
  19 which setting is fastest. It will also test whether performance can
  20 be enhanced by shifting load from the reciprocal to the real space
  21 part of the Ewald sum.
  22 Simply pass your <tt>.<a href="tpr.html">tpr</a></tt> file to g_tune_pme together with other options
  23 for <a href="mdrun.html">mdrun</a> as needed.<p>
  24 Which executables are used can be set in the environment variables
  25 MPIRUN and MDRUN. If these are not present, 'mpirun' and '<a href="mdrun.html">mdrun</a>'
  26 will be used as defaults. Note that for certain MPI frameworks you
  27 need to provide a machine- or hostfile. This can also be passed
  28 via the MPIRUN variable, e.g.
  29 'export MPIRUN="/usr/local/mpirun -machinefile hosts"'<p>
  30 Please call g_tune_pme with the normal options you would pass to
  31 <a href="mdrun.html">mdrun</a> and add <tt>-np</tt> for the number of processors to perform the
  32 tests on, or <tt>-nt</tt> for the number of threads. You can also add <tt>-r</tt>
  33 to repeat each test several times to get better statistics. <p>
  34 g_tune_pme can test various real space / reciprocal space workloads
  35 for you. With <tt>-ntpr</tt> you control how many extra <tt>.<a href="tpr.html">tpr</a></tt> files will be
  36 written with enlarged cutoffs and smaller fourier grids respectively.
  37 Typically, the first test (no. 0) will be with the settings from the input
  38 <tt>.<a href="tpr.html">tpr</a></tt> file; the last test (no. <tt>ntpr</tt>) will have cutoffs multiplied
  39 by (and at the same time fourier grid dimensions divided by) the scaling
  40 factor <tt>-fac</tt> (default 1.2). The remaining <tt>.<a href="tpr.html">tpr</a></tt> files will have equally
  41 spaced values inbetween these extremes. Note that you can set <tt>-ntpr</tt> to 1
  42 if you just want to find the optimal number of PME-only nodes; in that case
  43 your input <tt>.<a href="tpr.html">tpr</a></tt> file will remain unchanged.<p>
  44 For the benchmark runs, the default of 1000 time steps should suffice for most
  45 MD systems. The dynamic load balancing needs about 100 time steps
  46 to adapt to local load imbalances, therefore the time step counters
  47 are by default reset after 100 steps. For large systems
  48 (&gt;1M atoms) you may have to set <tt>-resetstep</tt> to a higher value.
  49 From the 'DD' load imbalance entries in the md.<a href="log.html">log</a> output file you
  50 can tell after how many steps the load is sufficiently balanced.<p>Example call: <tt>g_tune_pme -np 64 -s protein.<a href="tpr.html">tpr</a> -launch</tt><p>
  51 After calling <a href="mdrun.html">mdrun</a> several times, detailed performance information
  52 is available in the output file perf.out.
  53 Note that during the benchmarks a couple of temporary files are written
  54 (options -b*), these will be automatically deleted after each test.<p>
  55 If you want the simulation to be started automatically with the
  56 optimized parameters, use the command line option <tt>-launch</tt>.<p>
  57 <P>
  58 <H3>Files</H3>
  59 <TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
  60 <TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
  61 <TR><TD ALIGN=RIGHT> <b><tt>-p</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="out.html">    perf.out</a></tt> </TD><TD> Output </TD><TD> Generic output file </TD></TR>
  62 <TR><TD ALIGN=RIGHT> <b><tt>-err</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="log.html">  errors.log</a></tt> </TD><TD> Output </TD><TD> Log file </TD></TR>
  63 <TR><TD ALIGN=RIGHT> <b><tt>-so</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html">   tuned.tpr</a></tt> </TD><TD> Output </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>
  64 <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>
  65 <TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html">    traj.trr</a></tt> </TD><TD> Output </TD><TD> Full precision trajectory: <a href="trr.html">trr</a> <a href="trj.html">trj</a> cpt </TD></TR>
  66 <TR><TD ALIGN=RIGHT> <b><tt>-x</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xtc.html">    traj.xtc</a></tt> </TD><TD> Output, Opt. </TD><TD> Compressed trajectory (portable xdr format) </TD></TR>
  67 <TR><TD ALIGN=RIGHT> <b><tt>-cpi</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="cpt.html">   state.cpt</a></tt> </TD><TD> Input, Opt. </TD><TD> Checkpoint file </TD></TR>
  68 <TR><TD ALIGN=RIGHT> <b><tt>-cpo</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="cpt.html">   state.cpt</a></tt> </TD><TD> Output, Opt. </TD><TD> Checkpoint file </TD></TR>
  69 <TR><TD ALIGN=RIGHT> <b><tt>-c</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> confout.gro</a></tt> </TD><TD> Output </TD><TD> Structure file: <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> etc. </TD></TR>
  70 <TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="edr.html">    ener.edr</a></tt> </TD><TD> Output </TD><TD> Energy file </TD></TR>
  71 <TR><TD ALIGN=RIGHT> <b><tt>-g</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="log.html">      md.log</a></tt> </TD><TD> Output </TD><TD> Log file </TD></TR>
  72 <TR><TD ALIGN=RIGHT> <b><tt>-dhdl</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">    dhdl.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
  73 <TR><TD ALIGN=RIGHT> <b><tt>-field</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">   field.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
  74 <TR><TD ALIGN=RIGHT> <b><tt>-table</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">   table.xvg</a></tt> </TD><TD> Input, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
  75 <TR><TD ALIGN=RIGHT> <b><tt>-tablep</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">  tablep.xvg</a></tt> </TD><TD> Input, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
  76 <TR><TD ALIGN=RIGHT> <b><tt>-tableb</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">   table.xvg</a></tt> </TD><TD> Input, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
  77 <TR><TD ALIGN=RIGHT> <b><tt>-rerun</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html">   rerun.xtc</a></tt> </TD><TD> Input, Opt. </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>
  78 <TR><TD ALIGN=RIGHT> <b><tt>-tpi</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">     tpi.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
  79 <TR><TD ALIGN=RIGHT> <b><tt>-tpid</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> tpidist.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
  80 <TR><TD ALIGN=RIGHT> <b><tt>-ei</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="edi.html">     sam.edi</a></tt> </TD><TD> Input, Opt. </TD><TD> ED sampling input </TD></TR>
  81 <TR><TD ALIGN=RIGHT> <b><tt>-eo</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="edo.html">     sam.edo</a></tt> </TD><TD> Output, Opt. </TD><TD> ED sampling output </TD></TR>
  82 <TR><TD ALIGN=RIGHT> <b><tt>-j</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="gct.html">    wham.gct</a></tt> </TD><TD> Input, Opt. </TD><TD> General coupling stuff </TD></TR>
  83 <TR><TD ALIGN=RIGHT> <b><tt>-jo</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="gct.html">     bam.gct</a></tt> </TD><TD> Output, Opt. </TD><TD> General coupling stuff </TD></TR>
  84 <TR><TD ALIGN=RIGHT> <b><tt>-ffout</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">     gct.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
  85 <TR><TD ALIGN=RIGHT> <b><tt>-devout</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">deviatie.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
  86 <TR><TD ALIGN=RIGHT> <b><tt>-runav</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> runaver.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
  87 <TR><TD ALIGN=RIGHT> <b><tt>-px</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">   pullx.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
  88 <TR><TD ALIGN=RIGHT> <b><tt>-pf</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">   pullf.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
  89 <TR><TD ALIGN=RIGHT> <b><tt>-mtx</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="mtx.html">      nm.mtx</a></tt> </TD><TD> Output, Opt. </TD><TD> Hessian matrix </TD></TR>
  90 <TR><TD ALIGN=RIGHT> <b><tt>-dn</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html">  dipole.ndx</a></tt> </TD><TD> Output, Opt. </TD><TD> Index file </TD></TR>
  91 <TR><TD ALIGN=RIGHT> <b><tt>-bo</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html">   bench.trr</a></tt> </TD><TD> Output </TD><TD> Full precision trajectory: <a href="trr.html">trr</a> <a href="trj.html">trj</a> cpt </TD></TR>
  92 <TR><TD ALIGN=RIGHT> <b><tt>-bx</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xtc.html">   bench.xtc</a></tt> </TD><TD> Output </TD><TD> Compressed trajectory (portable xdr format) </TD></TR>
  93 <TR><TD ALIGN=RIGHT> <b><tt>-bcpo</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="cpt.html">   bench.cpt</a></tt> </TD><TD> Output </TD><TD> Checkpoint file </TD></TR>
  94 <TR><TD ALIGN=RIGHT> <b><tt>-bc</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html">   bench.gro</a></tt> </TD><TD> Output </TD><TD> Structure file: <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> etc. </TD></TR>
  95 <TR><TD ALIGN=RIGHT> <b><tt>-be</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="edr.html">   bench.edr</a></tt> </TD><TD> Output </TD><TD> Energy file </TD></TR>
  96 <TR><TD ALIGN=RIGHT> <b><tt>-bg</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="log.html">   bench.log</a></tt> </TD><TD> Output </TD><TD> Log file </TD></TR>
  97 <TR><TD ALIGN=RIGHT> <b><tt>-beo</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="edo.html">   bench.edo</a></tt> </TD><TD> Output, Opt. </TD><TD> ED sampling output </TD></TR>
  98 <TR><TD ALIGN=RIGHT> <b><tt>-bdhdl</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">benchdhdl.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
  99 <TR><TD ALIGN=RIGHT> <b><tt>-bfield</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">benchfld.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
 100 <TR><TD ALIGN=RIGHT> <b><tt>-btpi</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">benchtpi.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
 101 <TR><TD ALIGN=RIGHT> <b><tt>-btpid</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">benchtpid.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
 102 <TR><TD ALIGN=RIGHT> <b><tt>-bjo</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="gct.html">   bench.gct</a></tt> </TD><TD> Output, Opt. </TD><TD> General coupling stuff </TD></TR>
 103 <TR><TD ALIGN=RIGHT> <b><tt>-bffout</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">benchgct.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
 104 <TR><TD ALIGN=RIGHT> <b><tt>-bdevout</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">benchdev.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
 105 <TR><TD ALIGN=RIGHT> <b><tt>-brunav</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">benchrnav.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
 106 <TR><TD ALIGN=RIGHT> <b><tt>-bpx</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> benchpx.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
 107 <TR><TD ALIGN=RIGHT> <b><tt>-bpf</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> benchpf.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
 108 <TR><TD ALIGN=RIGHT> <b><tt>-bmtx</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="mtx.html">  benchn.mtx</a></tt> </TD><TD> Output, Opt. </TD><TD> Hessian matrix </TD></TR>
 109 <TR><TD ALIGN=RIGHT> <b><tt>-bdn</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html">   bench.ndx</a></tt> </TD><TD> Output, Opt. </TD><TD> Index file </TD></TR>
 110 </TABLE>
 111 <P>
 112 <H3>Other options</H3>
 113 <TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
 114 <TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
 115 <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>
 116 <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>
 117 <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>
 118 <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>
 119 <TR><TD ALIGN=RIGHT> <b><tt>-np</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1</tt> </TD><TD> Number of nodes to run the tests on (must be &gt; 2 for separate PME nodes) </TD></TD>
 120 <TR><TD ALIGN=RIGHT> <b><tt>-npstring</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>-np</tt> </TD><TD> Specify the number of processors to $MPIRUN using this string: <tt>-np</tt>, <tt>-n</tt> or <tt>none</tt> </TD></TD>
 121 <TR><TD ALIGN=RIGHT> <b><tt>-nt</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1</tt> </TD><TD> Number of threads to run the tests on (turns MPI & mpirun off) </TD></TD>
 122 <TR><TD ALIGN=RIGHT> <b><tt>-r</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>2</tt> </TD><TD> Repeat each test this often </TD></TD>
 123 <TR><TD ALIGN=RIGHT> <b><tt>-max</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0.5   </tt> </TD><TD> Max fraction of PME nodes to test with </TD></TD>
 124 <TR><TD ALIGN=RIGHT> <b><tt>-min</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0.25  </tt> </TD><TD> Min fraction of PME nodes to test with </TD></TD>
 125 <TR><TD ALIGN=RIGHT> <b><tt>-npme</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>auto</tt> </TD><TD> Benchmark all possible values for -npme or just the subset that is expected to perform well: <tt>auto</tt>, <tt>all</tt> or <tt>subset</tt> </TD></TD>
 126 <TR><TD ALIGN=RIGHT> <b><tt>-upfac</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>1.2   </tt> </TD><TD> Upper limit for rcoulomb scaling factor (Note that rcoulomb upscaling results in fourier grid downscaling) </TD></TD>
 127 <TR><TD ALIGN=RIGHT> <b><tt>-downfac</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>1     </tt> </TD><TD> Lower limit for rcoulomb scaling factor </TD></TD>
 128 <TR><TD ALIGN=RIGHT> <b><tt>-ntpr</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Number of <a href="tpr.html">tpr</a> files to benchmark. Create these many files with scaling factors ranging from 1.0 to fac. If &lt; 1, automatically choose the number of <a href="tpr.html">tpr</a> files to test </TD></TD>
 129 <TR><TD ALIGN=RIGHT> <b><tt>-four</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0     </tt> </TD><TD> Use this fourierspacing value instead of the grid found in the <a href="tpr.html">tpr</a> input file. (Spacing applies to a scaling factor of 1.0 if multiple <a href="tpr.html">tpr</a> files are written) </TD></TD>
 130 <TR><TD ALIGN=RIGHT> <b><tt>-steps</tt></b> </TD><TD ALIGN=RIGHT> step </TD><TD ALIGN=RIGHT> <tt>1000</tt> </TD><TD> Take timings for these many steps in the benchmark runs </TD></TD>
 131 <TR><TD ALIGN=RIGHT> <b><tt>-resetstep</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>100</tt> </TD><TD> Let dlb equilibrate these many steps before timings are taken (reset cycle counters after these many steps) </TD></TD>
 132 <TR><TD ALIGN=RIGHT> <b><tt>-simsteps</tt></b> </TD><TD ALIGN=RIGHT> step </TD><TD ALIGN=RIGHT> <tt>-1</tt> </TD><TD> If non-negative, perform these many steps in the real run (overwrite nsteps from <a href="tpr.html">tpr</a>, add cpt steps) </TD></TD>
 133 <TR><TD ALIGN=RIGHT> <b><tt>-[no]launch</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Lauch the real simulation after optimization </TD></TD>
 134 <TR><TD ALIGN=RIGHT> <b><tt>-deffnm</tt></b> </TD><TD ALIGN=RIGHT> string </TD><TD ALIGN=RIGHT> <tt></tt> </TD><TD> Set the default filename for all file options at launch time </TD></TD>
 135 <TR><TD ALIGN=RIGHT> <b><tt>-ddorder</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>interleave</tt> </TD><TD> DD node order: <tt>interleave</tt>, <tt>pp_pme</tt> or <tt>cartesian</tt> </TD></TD>
 136 <TR><TD ALIGN=RIGHT> <b><tt>-[no]ddcheck</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>yes   </tt> </TD><TD> Check for all bonded interactions with DD </TD></TD>
 137 <TR><TD ALIGN=RIGHT> <b><tt>-rdd</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0     </tt> </TD><TD> The maximum distance for bonded interactions with DD (nm), 0 is determine from initial coordinates </TD></TD>
 138 <TR><TD ALIGN=RIGHT> <b><tt>-rcon</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0     </tt> </TD><TD> Maximum distance for P-LINCS (nm), 0 is estimate </TD></TD>
 139 <TR><TD ALIGN=RIGHT> <b><tt>-dlb</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>auto</tt> </TD><TD> Dynamic load balancing (with DD): <tt>auto</tt>, <tt>no</tt> or <tt>yes</tt> </TD></TD>
 140 <TR><TD ALIGN=RIGHT> <b><tt>-dds</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0.8   </tt> </TD><TD> Minimum allowed dlb scaling of the DD cell size </TD></TD>
 141 <TR><TD ALIGN=RIGHT> <b><tt>-gcom</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>-1</tt> </TD><TD> Global communication frequency </TD></TD>
 142 <TR><TD ALIGN=RIGHT> <b><tt>-[no]v</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Be loud and noisy </TD></TD>
 143 <TR><TD ALIGN=RIGHT> <b><tt>-[no]compact</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>yes   </tt> </TD><TD> Write a compact <a href="log.html">log</a> file </TD></TD>
 144 <TR><TD ALIGN=RIGHT> <b><tt>-[no]seppot</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Write separate V and dVdl terms for each interaction type and node to the <a href="log.html">log</a> file(s) </TD></TD>
 145 <TR><TD ALIGN=RIGHT> <b><tt>-pforce</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>-1    </tt> </TD><TD> Print all forces larger than this (kJ/mol nm) </TD></TD>
 146 <TR><TD ALIGN=RIGHT> <b><tt>-[no]reprod</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Try to avoid optimizations that affect binary reproducibility </TD></TD>
 147 <TR><TD ALIGN=RIGHT> <b><tt>-cpt</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>15    </tt> </TD><TD> Checkpoint interval (minutes) </TD></TD>
 148 <TR><TD ALIGN=RIGHT> <b><tt>-[no]cpnum</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Keep and number checkpoint files </TD></TD>
 149 <TR><TD ALIGN=RIGHT> <b><tt>-[no]append</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>yes   </tt> </TD><TD> Append to previous output files when continuing from checkpoint instead of adding the simulation part number to all file names (for launch only) </TD></TD>
 150 <TR><TD ALIGN=RIGHT> <b><tt>-maxh</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>-1    </tt> </TD><TD> Terminate after 0.99 times this time (hours) </TD></TD>
 151 <TR><TD ALIGN=RIGHT> <b><tt>-multi</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Do multiple simulations in parallel </TD></TD>
 152 <TR><TD ALIGN=RIGHT> <b><tt>-replex</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Attempt replica exchange every # steps </TD></TD>
 153 <TR><TD ALIGN=RIGHT> <b><tt>-reseed</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>-1</tt> </TD><TD> Seed for replica exchange, -1 is generate a seed </TD></TD>
 154 <TR><TD ALIGN=RIGHT> <b><tt>-[no]ionize</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Do a simulation including the effect of an X-Ray bombardment on your system </TD></TD>
 155 </TABLE>
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