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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>mdrun</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>
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  15 <H3>Description</H3>
  16 <p>
  17 The mdrun program is the main computational chemistry engine
  18 within GROMACS. Obviously, it performs Molecular Dynamics simulations,
  19 but it can also perform Stochastic Dynamics, Energy Minimization,
  20 test particle insertion or (re)calculation of energies.
  21 Normal mode analysis is another option. In this case mdrun
  22 builds a Hessian matrix from single conformation.
  23 For usual Normal Modes-like calculations, make sure that
  24 the structure provided is properly energy-minimized.
  25 The generated matrix can be diagonalized by <a href="g_nmeig.html">g_nmeig</a>.<p>
  26 The mdrun program reads the run input file (<tt>-s</tt>)
  27 and distributes the topology over nodes if needed.
  28 mdrun produces at least four output files.
  29 A single <a href="log.html">log</a> file (<tt>-g</tt>) is written, unless the option
  30 <tt>-seppot</tt> is used, in which case each node writes a <a href="log.html">log</a> file.
  31 The trajectory file (<tt>-o</tt>), contains coordinates, velocities and
  32 optionally forces.
  33 The structure file (<tt>-c</tt>) contains the coordinates and
  34 velocities of the last step.
  35 The energy file (<tt>-e</tt>) contains energies, the temperature,
  36 pressure, etc, a lot of these things are also printed in the <a href="log.html">log</a> file.
  37 Optionally coordinates can be written to a compressed trajectory file
  38 (<tt>-x</tt>).<p>
  39 The option <tt>-dhdl</tt> is only used when free energy calculation is
  40 turned on.<p>
  41 When mdrun is started using MPI with more than 1 node, parallelization
  42 is used. By default domain decomposition is used, unless the <tt>-pd</tt>
  43 option is set, which selects particle decomposition.<p>
  44 With domain decomposition, the spatial decomposition can be set
  45 with option <tt>-dd</tt>. By default mdrun selects a good decomposition.
  46 The user only needs to change this when the system is very inhomogeneous.
  47 Dynamic load balancing is set with the option <tt>-dlb</tt>,
  48 which can give a significant performance improvement,
  49 especially for inhomogeneous systems. The only disadvantage of
  50 dynamic load balancing is that runs are no longer binary reproducible,
  51 but in most cases this is not important.
  52 By default the dynamic load balancing is automatically turned on
  53 when the measured performance loss due to load imbalance is 5% or more.
  54 At low parallelization these are the only important options
  55 for domain decomposition.
  56 At high parallelization the options in the next two sections
  57 could be important for increasing the performace.
  58 <p>
  59 When PME is used with domain decomposition, separate nodes can
  60 be assigned to do only the PME mesh calculation;
  61 this is computationally more efficient starting at about 12 nodes.
  62 The number of PME nodes is set with option <tt>-npme</tt>,
  63 this can not be more than half of the nodes.
  64 By default mdrun makes a guess for the number of PME
  65 nodes when the number of nodes is larger than 11 or performance wise
  66 not compatible with the PME grid x dimension.
  67 But the user should optimize npme. Performance statistics on this issue
  68 are written at the end of the <a href="log.html">log</a> file.
  69 For good load balancing at high parallelization, the PME grid x and y
  70 dimensions should be divisible by the number of PME nodes
  71 (the simulation will run correctly also when this is not the case).
  72 <p>
  73 This section lists all options that affect the domain decomposition.
  74 <br>
  75 Option <tt>-rdd</tt> can be used to set the required maximum distance
  76 for inter charge-group bonded interactions.
  77 Communication for two-body bonded interactions below the non-bonded
  78 cut-off distance always comes for free with the non-bonded communication.
  79 Atoms beyond the non-bonded cut-off are only communicated when they have
  80 missing bonded interactions; this means that the extra cost is minor
  81 and nearly indepedent of the value of <tt>-rdd</tt>.
  82 With dynamic load balancing option <tt>-rdd</tt> also sets
  83 the lower limit for the domain decomposition cell sizes.
  84 By default <tt>-rdd</tt> is determined by mdrun based on
  85 the initial coordinates. The chosen value will be a balance
  86 between interaction range and communication cost.
  87 <br>
  88 When inter charge-group bonded interactions are beyond
  89 the bonded cut-off distance, mdrun terminates with an error message.
  90 For pair interactions and tabulated bonds
  91 that do not generate exclusions, this check can be turned off
  92 with the option <tt>-noddcheck</tt>.
  93 <br>
  94 When constraints are present, option <tt>-rcon</tt> influences
  95 the cell size limit as well.
  96 Atoms connected by NC constraints, where NC is the LINCS order plus 1,
  97 should not be beyond the smallest cell size. A error message is
  98 generated when this happens and the user should change the decomposition
  99 or decrease the LINCS order and increase the number of LINCS iterations.
 100 By default mdrun estimates the minimum cell size required for P-LINCS
 101 in a conservative fashion. For high parallelization it can be useful
 102 to set the distance required for P-LINCS with the option <tt>-rcon</tt>.
 103 <br>
 104 The <tt>-dds</tt> option sets the minimum allowed x, y and/or z scaling
 105 of the cells with dynamic load balancing. mdrun will ensure that
 106 the cells can scale down by at least this factor. This option is used
 107 for the automated spatial decomposition (when not using <tt>-dd</tt>)
 108 as well as for determining the number of grid pulses, which in turn
 109 sets the minimum allowed cell size. Under certain circumstances
 110 the value of <tt>-dds</tt> might need to be adjusted to account for
 111 high or low spatial inhomogeneity of the system.
 112 <p>
 113 The option <tt>-gcom</tt> can be used to only do global communication
 114 every n steps.
 115 This can improve performance for highly parallel simulations
 116 where this global communication step becomes the bottleneck.
 117 For a global thermostat and/or barostat the temperature
 118 and/or pressure will also only be updated every -gcom steps.
 119 By default it is set to the minimum of nstcalcenergy and nstlist.<p>
 120 With <tt>-rerun</tt> an input trajectory can be given for which
 121 forces and energies will be (re)calculated. Neighbor searching will be
 122 performed for every frame, unless <tt>nstlist</tt> is zero
 123 (see the <tt>.<a href="mdp.html">mdp</a></tt> file).<p>
 124 ED (essential dynamics) sampling is switched on by using the <tt>-ei</tt>
 125 flag followed by an <tt>.<a href="edi.html">edi</a></tt> file.
 126 The <tt>.<a href="edi.html">edi</a></tt> file can be produced using options in the essdyn
 127 menu of the WHAT IF program. mdrun produces a <tt>.<a href="edo.html">edo</a></tt> file that
 128 contains projections of positions, velocities and forces onto selected
 129 eigenvectors.<p>
 130 When user-defined potential functions have been selected in the
 131 <tt>.<a href="mdp.html">mdp</a></tt> file the <tt>-table</tt> option is used to pass mdrun
 132 a formatted table with potential functions. The file is read from
 133 either the current directory or from the GMXLIB directory.
 134 A number of pre-formatted tables are presented in the GMXLIB dir,
 135 for 6-8, 6-9, 6-10, 6-11, 6-12 Lennard Jones potentials with
 136 normal Coulomb.
 137 When pair interactions are present a separate table for pair interaction
 138 functions is read using the <tt>-tablep</tt> option.<p>
 139 When tabulated bonded functions are present in the topology,
 140 interaction functions are read using the <tt>-tableb</tt> option.
 141 For each different tabulated interaction type the table file name is
 142 modified in a different way: before the file extension an underscore is
 143 appended, then a b for bonds, an a for angles or a d for dihedrals
 144 and finally the table number of the interaction type.<p>
 145 The options <tt>-px</tt> and <tt>-pf</tt> are used for writing pull COM
 146 coordinates and forces when pulling is selected
 147 in the <tt>.<a href="mdp.html">mdp</a></tt> file.<p>
 148 With <tt>-multi</tt> multiple systems are simulated in parallel.
 149 As many input files are required as the number of systems.
 150 The system number is appended to the run input and each output filename,
 151 for instance topol.<a href="tpr.html">tpr</a> becomes topol0.<a href="tpr.html">tpr</a>, topol1.<a href="tpr.html">tpr</a> etc.
 152 The number of nodes per system is the total number of nodes
 153 divided by the number of systems.
 154 One use of this option is for NMR refinement: when distance
 155 or orientation restraints are present these can be ensemble averaged
 156 over all the systems.<p>
 157 With <tt>-replex</tt> replica exchange is attempted every given number
 158 of steps. The number of replicas is set with the <tt>-multi</tt> option,
 159 see above.
 160 All run input files should use a different coupling temperature,
 161 the order of the files is not important. The random seed is set with
 162 <tt>-reseed</tt>. The velocities are scaled and neighbor searching
 163 is performed after every exchange.<p>
 164 Finally some experimental algorithms can be tested when the
 165 appropriate options have been given. Currently under
 166 investigation are: polarizability, and X-Ray bombardments.
 167 <p>
 168 The option <tt>-pforce</tt> is useful when you suspect a simulation
 169 crashes due to too large forces. With this option coordinates and
 170 forces of atoms with a force larger than a certain value will
 171 be printed to stderr.
 172 <p>
 173 Checkpoints containing the complete state of the system are written
 174 at regular intervals (option <tt>-cpt</tt>) to the file <tt>-cpo</tt>,
 175 unless option <tt>-cpt</tt> is set to -1.
 176 The previous checkpoint is backed up to <tt>state_prev.cpt</tt> to
 177 make sure that a recent state of the system is always available,
 178 even when the simulation is terminated while writing a checkpoint.
 179 With <tt>-cpnum</tt> all checkpoint files are kept and appended
 180 with the step number.
 181 A simulation can be continued by reading the full state from file
 182 with option <tt>-cpi</tt>. This option is intelligent in the way that
 183 if no checkpoint file is found, Gromacs just assumes a normal run and
 184 starts from the first step of the <a href="tpr.html">tpr</a> file. By default the output
 185 will be appending to the existing output files. The checkpoint file
 186 contains checksums of all output files, such that you will never
 187 loose data when some output files are modified, corrupt or removed.
 188 There are three scenarios with <tt>-cpi</tt>:<br>
 189 * no files with matching names are present: new output files are written<br>
 190 * all files are present with names and checksums matching those stored
 191 in the checkpoint file: files are appended<br>
 192 * otherwise no files are modified and a fatal error is generated<br>
 193 With <tt>-noappend</tt> new output files are opened and the simulation
 194 part number is added to all output file names.
 195 Note that in all cases the checkpoint file itself is not renamed
 196 and will be overwritten, unless its name does not match
 197 the <tt>-cpo</tt> option.
 198 <p>
 199 With checkpointing the output is appended to previously written
 200 output files, unless <tt>-noappend</tt> is used or none of the previous
 201 output files are present (except for the checkpoint file).
 202 The integrity of the files to be appended is verified using checksums
 203 which are stored in the checkpoint file. This ensures that output can
 204 not be mixed up or corrupted due to file appending. When only some
 205 of the previous output files are present, a fatal error is generated
 206 and no old output files are modified and no new output files are opened.
 207 The result with appending will be the same as from a single run.
 208 The contents will be binary identical, unless you use a different number
 209 of nodes or dynamic load balancing or the FFT library uses optimizations
 210 through timing.
 211 <p>
 212 With option <tt>-maxh</tt> a simulation is terminated and a checkpoint
 213 file is written at the first neighbor search step where the run time
 214 exceeds <tt>-maxh</tt>*0.99 hours.
 215 <p>
 216 When mdrun receives a TERM signal, it will set nsteps to the current
 217 step plus one. When mdrun receives an INT signal (e.g. when ctrl+C is
 218 pressed), it will stop after the next neighbor search step
 219 (with nstlist=0 at the next step).
 220 In both cases all the usual output will be written to file.
 221 When running with MPI, a signal to one of the mdrun processes
 222 is sufficient, this signal should not be sent to mpirun or
 223 the mdrun process that is the parent of the others.
 224 <p>
 225 When mdrun is started with MPI, it does not run niced by default.
 226 <P>
 227 <H3>Files</H3>
 228 <TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
 229 <TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
 230 <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>
 231 <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>
 232 <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>
 233 <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>
 234 <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>
 235 <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>
 236 <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>
 237 <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>
 238 <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>
 239 <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>
 240 <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>
 241 <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>
 242 <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>
 243 <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>
 244 <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>
 245 <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>
 246 <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>
 247 <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>
 248 <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>
 249 <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>
 250 <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>
 251 <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>
 252 <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>
 253 <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>
 254 <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>
 255 <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>
 256 <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>
 257 </TABLE>
 258 <P>
 259 <H3>Other options</H3>
 260 <TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
 261 <TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
 262 <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>
 263 <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>
 264 <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>
 265 <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 </TD></TD>
 266 <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>
 267 <TR><TD ALIGN=RIGHT> <b><tt>-[no]pd</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Use particle decompostion </TD></TD>
 268 <TR><TD ALIGN=RIGHT> <b><tt>-dd</tt></b> </TD><TD ALIGN=RIGHT> vector </TD><TD ALIGN=RIGHT> <tt>0 0 0</tt> </TD><TD> Domain decomposition grid, 0 is optimize </TD></TD>
 269 <TR><TD ALIGN=RIGHT> <b><tt>-nt</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Number of threads to start (0 is guess) </TD></TD>
 270 <TR><TD ALIGN=RIGHT> <b><tt>-npme</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>-1</tt> </TD><TD> Number of separate nodes to be used for PME, -1 is guess </TD></TD>
 271 <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>
 272 <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>
 273 <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>
 274 <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>
 275 <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>
 276 <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>
 277 <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>
 278 <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>
 279 <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>
 280 <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>
 281 <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>
 282 <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>
 283 <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>
 284 <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>
 285 <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 </TD></TD>
 286 <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>
 287 <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>
 288 <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>
 289 <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>
 290 <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>
 291 </TABLE>
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