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   8 <h2>Contents</h2>
   9 <ul>
  10 <li><a href="#start">Getting started</a>
  11 <ul>
  12         <li><a href="#setup">Setting up your environment</a>
  13         <li><a href="#examples">Examples</a>
  14 </ul>
  15 <li><a href="#demo">GMX demo</a>
  16 <ul>
  17         <li><a href="#top">Molecular topology file</a>
  18         <li><a href="#gro">Molecular structure file</a>
  19         <li><a href="#mdp">Molecular dynamics parameter file</a>
  20         <li><a href="#ndx">Index file</a>
  21         <li><a href="#tpr">Run input file</a>
  22         <li><a href="#trx">Trajectory file</a>
  23 </ul>
  24 <li><a href="#water">Water</a>
  25 <li><a href="#spep">Ribonuclease S-Peptide</a>
  26 <ul>
  27         <li><a href="#pdb2gmx">Generating a topology file</a>
  28         <li><a href="#solvate">Solvate the peptide</a>
  29         <li><a href="#indexfile">Generate an index file</a>
  30         <li><a href="#em">Energy minimization</a>
  31         <li><a href="#posres">Molecular dynamics with position restraints</a>
  32         <li><a href="#full">Unrestrained molecular dynamics</a>
  33         <li><a href="#analysis">Analysis of trajectory files</a>
  34 </ul>
  35 <li><a href="#you">Your own system</a>
  36 <li><a href="#info">More Info</a>
  37 <li><a href="#ref">References</a>
  38 </ul>
  39
  40 <P>
  41 More info can be found in the
  42 <A HREF="flow.html">flowchart</A>
  43 (for a quick overview) and the
  44 <A HREF="../gmxfaq.html">GMX FAQ</A>.
  45 </P>
  46
  47 <br><hr><br>
  48
  49 <a name="start"><H1>Getting started.</A></H1>
  50
  51 In this chapter we assume the reader is familiar with Molecular
  52 Dynamics and familiar with Unix, including the use of a text editor
  53 such as <tt>emacs</tt> or <tt>vi</tt>. We furthermore assume the
  54 software is installed properly on your system. When you see a line
  55 like
  56 <PRE>
  57 % ls -l
  58 </PRE>
  59 you are supposed to type the contents of that line (not the
  60 <TT>%</TT>) on your computer.
  61
  62 <P>We will also assume that you know where your version of GROMACS is
  63 installed. For local users in the Groningen MD group that is simply
  64 '~gmx', e.g. the GMXRC is located in ~gmx/GMXRC. For other users that
  65 is probably not the case, contact your local system administrator for
  66 more information. The directories named in this section are valid for the
  67 Groningen MD group.
  68
  69 <P><H2><A NAME="setup">Setting up your environment</A></H2>
  70
  71 Edit your <TT>.cshrc</TT> file to include the following statement:
  72 <PRE>
  73 source ~gmx/GMXRC
  74 </PRE>
  75 which has some (system dependent) PATH settings etcetera. Then type
  76 <PRE>
  77 % source ~gmx/GMXRC
  78 </PRE>
  79 to start right away, or, alternatively
  80 log off and on again to automatically source the environment.
  81 <P>
  82 Check if you now have the proper environment by
  83 <PRE>
  84 % echo $GMXHOME
  85 </PRE>
  86 It should read something like:
  87 <PRE>
  88 /home/gmx/gmx2.0
  89 </PRE>
  90 This is the directory in which the binaries and
  91 library files live. If you see nothing (a blank line) something is
  92 wrong with the installation, check with your system manager, or (if
  93 <EM>you</EM> are the system manager) you did something wrong
  94 somewhere <b>:(</b>
  95
  96 <P><H2><A NAME="examples">Examples.</A></H2>
  97 Before starting the examples, you have to copy all the neccesary
  98 files, to your own directory. Chdir to the directory you want to put
  99 the examples directory. This directory (named <tt>tutor</tt>)
 100 will need
 101 about 20 MB of disk space, when it is completely filled.
 102 <PRE>
 103 % cd ``your own directory''
 104 </PRE>
 105 then copy the examples:
 106 <PRE>
 107 % cp -r ~gmx/home2.0/tutor .
 108 </PRE>
 109 (NOTE: include the ``<TT>.</TT>'') You now have a subdirectory
 110 <tt>tutor</tt>. Move there
 111 <PRE>
 112 % cd tutor
 113 </PRE>
 114 and view the contents of this directory
 115 <PRE>
 116 % ls -l
 117 </PRE>
 118 If all is well you will have five subdirectories with examples
 119 with names like <tt>gmxdemo</tt>, <tt>nmr1</tt>, <tt>nmr2</tt>,
 120 <tt>speptide</tt> and <tt>water</tt>.
 121 <P>
 122 You are encouraged to look up the different programs and
 123 file formats in <a href="../online.html">
 124 the online manual</a> while you are browsing through the examples.</p>
 125
 126 <br><hr><br>
 127
 128 <P><H1><A NAME="demo">GMX demo.</A></H1>
 129 The demo is designed to demonstrate the user-friendlyness
 130 of the GROMACS software package. Start the demo by going
 131 to your <tt>tutor/gmxdemo</tt> directory:
 132 <PRE>
 133 % cd tutor/gmxdemo
 134 </PRE> Start the demo:
 135 <PRE>
 136 % demo
 137 </PRE>
 138 This demo handles a complete Molecular Dynamics simulation of a
 139 peptide in water, starting from a
 140 <a href="pdb.html">pdb</a> structure. When you run a
 141 Molecular Dynamics simulation with GROMACS you will encounter the
 142 following file formats:
 143
 144 <DL>
 145 <DT>
 146 <B><A NAME="top">Molecular Topology file (<TT><a href="top.html">.top</a></TT>)</A></B>
 147 <DD>
 148 The molecular topology file is generated by the program <TT>
 149 <a href="pdb2gmx.html">pdb2gmx</a></TT>. <a href="pdb2gmx.html">pdb2gmx</a> translates a <a href="pdb.html">pdb</a> structure file of any peptide
 150 or protein
 151 to a molecular topology file. This topology file contains a complete
 152 description of all the interactions in your peptide or protein.
 153 <P></P>
 154
 155 <DT>
 156 <B><A NAME="gro">Molecular Structure file (<TT><a href="gro.html">.gro</a></TT>, <TT><a href="pdb.html">.pdb</a></TT>)</A></B>
 157 <DD>
 158 When the <a href="pdb2gmx.html">pdb2gmx</a> program is executed to generate a molecular
 159 topology, it also translates the structure file (<TT><a href="pdb.html">.pdb</a></TT> file)
 160 to a gromos
 161 structure file (<TT><a href="gro.html">.gro</a></TT> file). The main difference between a
 162 <a href="pdb.html">pdb</a> file and a gromos file is their format and that
 163 a <TT><a href="gro.html">.gro</a></TT> file can also hold velocities. However, if you do not need the
 164 velocities, you can also use a <a href="pdb.html">pdb</a> file in all programs.
 165 To generate a box of solvent molecules
 166 around the peptide, the program
 167 <a href="genbox.html">genbox</a> is used. First the program
 168 <a href="editconf.html">editconf</a> should be used to
 169 define a box of appropriate size around the molecule.
 170 <a href="genbox.html">genbox</a>
 171 dissolves a solute molecule (the peptide) into any solvent (in this
 172 case water). The output of <TT><a href="genbox.html">genbox</a></TT> is a gromos structure file of
 173 the peptide dissolved in water. The <a href="genbox.html">genbox</a> program also changes the
 174 molecular topology file (generated by <a href="pdb2gmx.html">pdb2gmx</a>) to add solvent
 175 to the topology.
 176 <P></P>
 177
 178 <DT>
 179 <B><A NAME="mdp">Molecular Dynamics parameter file (<TT><a href="mdp_opt.html">.mdp</a></TT>)</A></B>
 180 <DD>
 181 The Molecular Dynamics Parameter (<TT><a href="mdp_opt.html">.mdp</a></TT>) file contains all
 182 information about the Molecular Dynamics simulation itself
 183 e.g. time-step, number of steps, temperature, pressure etc. The
 184 easiest way of handling such a file is by adapting a sample <TT><a href="mdp_opt.html">.mdp</a></TT>
 185 file. A <TT><a href="mdp.html">sample mdp file</a></TT>
 186 can be found online.
 187 <P></P>
 188
 189 <DT>
 190 <B><A NAME="ndx">Index file (<TT><a href="ndx.html">.ndx</a></TT>)</A></B>
 191 <DD>
 192 Sometimes you may need an index file to specify actions on groups of atoms
 193 (e.g. Temperature coupling, accelerations, freezing). Usually the default ibdex
 194 groups will be sufficient, so for this demo we will
 195 not consider the use of index files.
 196 <P></P>
 197
 198 <DT>
 199 <B><A NAME="tpr">Run input file (<TT><a href="tpr.html">.tpr</a></TT>)</A></B>
 200 <DD>
 201 The next step is to combine the molecular structure (<TT><a href="gro.html">.gro</a></TT> file),
 202 topology (<TT><a href="top.html">.top</a></TT> file) MD-parameters (<TT><a href="mdp_opt.html">.mdp</a></TT> file) and
 203 (optionally) the
 204 index file (<TT><a href="ndx.html">ndx</a></TT>) to generate a run input file (<TT><a href="tpr.html">.tpr</a></tt> extension or
 205 <TT><a href="tpb.html">.tpb</a></tt> if you don't have XDR).
 206 This file contains all information needed to start a simulation with GROMACS.
 207 The <a href="grompp.html">
 208 grompp</a> program processes all input files and generates the run input
 209 <tt><a href="tpr.html">.tpr</a></tt> file.
 210 <P></P>
 211
 212 <DT>
 213 <B><A NAME="trx">Trajectory file (<TT><a href="trr.html">.trr</a></TT></A>)</B>
 214 <DD>
 215 Once the run input file is available, we can start the
 216 simulation. The program which starts the simulation is called
 217 <a href="mdrun.html">mdrun</a>. The only input file
 218 of <TT><a href="mdrun.html">mdrun</a></TT> you usually need to start a run
 219 is the run input file (<TT><a href="tpr.html">.tpr</a></TT> file).
 220 The output files of
 221 <TT><a href="mdrun.html">mdrun</a></TT> are the
 222 trajectory file (<TT><a href="trr.html">.trr</a></TT> file
 223 or <TT><a href="trj.html">.trj</a></TT> if you don't have XDR) and a logfile (
 224 <TT><a href="log.html">.log</A></TT> file).
 225 <P></P>
 226
 227 </DL>
 228
 229 <br><hr><br>
 230
 231 <P><H1><A NAME="water">Water</A></H1>
 232 Now you are going to simulate 216 molecules of SPC water
 233 (<A HREF=#berendsen81>Berendsen <it>et al.</it>, 1981</A>)
 234 in a rectangular box. In this example the GROMACS
 235 software team already generated most of the neccesary input
 236 files. The files needed in this example are:
 237 <ul>
 238 <LI> Initial structure of a box of 216 water molecules (<TT><a href="gro.html">.gro</a></TT>)
 239 <LI> Topology file of water (<tt><a href="top.html">.top</a></tt>)
 240 <LI> Molecular Dynamics parameter file (<TT><a href="mdp_opt.html">.mdp</a></TT>)
 241 </ul>
 242 <P>
 243 Change your directory to <tt>tutor/water </tt>:
 244 <PRE>
 245 % cd tutor/water
 246 </PRE>
 247 Let's first have a look at the coordinate file:
 248 <PRE>
 249 % more <a href="gro.html">spc216.gro</a>
 250 </PRE>
 251 Or to view the water box graphically:
 252 <PRE>
 253 % rasmol <a href="pdb.html">spc216.pdb</a>
 254 </PRE>
 255 Have a look at the topology file:
 256 <PRE>
 257 % more <a href="top.html">water.top</a>
 258 </PRE>
 259 Have a look at the MD-parameters file:
 260 <PRE>
 261 % more <a href="mdp_opt.html">water.mdp</a>
 262 </PRE>
 263 Since all the neccesary files are available, we are going to,
 264 preprocess all the input files to create a run input
 265 (<TT><a href="tpr.html">.tpr</a></TT>) file.
 266 This run input file is the only input file for the
 267 MD-program <TT><a href="mdrun.html">mdrun</a></TT>.
 268 <PRE>
 269 % <a href="grompp.html">grompp</a> -f <a href="mdp_opt.html">water.mdp</a> -p <a href="top.html">water.top</a> -c <a href="gro.html">spc216.gro</a> -o <a href="tpr.html">water.tpr</a>
 270 </PRE>
 271 The run input file is only viewable with the program
 272 <TT><a href="gmxdump.html">gmxdump</a></TT>.
 273 In this way it is possible to check if the  preprocessor
 274 <TT><a href="grompp.html">grompp</a></TT> worked well.
 275 <PRE>
 276 % <a href="gmxdump.html">gmxdump</a> -s <a href="tpr.html">water.tpr</a> | more
 277 </PRE>
 278 Now it's time to start to the simulation
 279 <PRE>
 280 % <a href="mdrun.html">mdrun</a> -s <a href="tpr.html">water.tpr</a> -o <a href="trr.html">water.trr</a> -c <a href="gro.html">water_out.gro</a> -v -g water.log
 281 </PRE>
 282 After the MD simulation is finished, it is possible to view the
 283 trajectory with the <a href="ngmx.html">ngmx</a> program:
 284 <PRE>
 285 % <a href="ngmx.html">ngmx</a> -f <a href="trr.html">water.trr</a> -s <a href="tpr.html">water.tpr</a>
 286 </PRE>
 287 <P>
 288 When the program starts, you must select a group of atoms to view. In
 289 our case that will be "SOL" (for solvent) or "System", which is the
 290 same for a box of water as we have. Select one and click OK. Then
 291 select Display->Animate from the menu. Use the buttons to see your
 292 water moving (note: "Play" steps one frame forward; "Fast Forward"
 293 plays; "Rewind" skips back to the beginning of the trajectory).
 294 </P>
 295
 296 Calculate a radial distribution function of the Oxygen atoms. The
 297 index file <TT><a href="ndx.html">oxygen.ndx</a></TT>
 298 contains one group with all the oxygen atoms.
 299 <PRE>
 300 % <a href="g_rdf.html">g_rdf</a> -f <a href="trr.html">water.trr</a> -n <a href="ndx.html">oxygen.ndx</a> -o <a href="xvg.html">rdf.xvg</a> -s <a href="tpr.html">water.tpr</a>
 301 </PRE>
 302 view the output graph of <TT><a href="g_rdf.html">g_rdf</a></TT>
 303 <PRE>
 304 % xvgr <a href="xvg.html">rdf.xvg</a>
 305 </PRE>
 306 Which shows you the radial distribution function for Oxygen-Oxygen in
 307 SPC water. </p>
 308
 309 <br><hr><br>
 310
 311 <P><H1><A NAME="spep">Ribonuclease S-peptide.</A></H1>
 312 Ribonuclease A is a digestive enzyme, secreted by the pancreas. The enzyme
 313 can be cleaved by subtilisin at a single peptide bond to yield
 314 Ribonuclease-S, a catalytically active complex of an S-peptide moiety
 315 (residues 1-20) and an S-protein moiety (residues 21-124), bound together
 316 by multiple non-covalent links (<A HREF=#stryer88>Stryer, 1988</A>).
 317 <P>
 318 The S-Peptide has been studied in many ways, experimentally
 319 as well as theoretically (simulation) because of the high a-helix
 320 content in solution, which is remarkable in such a small peptide.
 321 <P>
 322 All the files of speptide are stored in the directory <TT>
 323 tutor/speptide</TT>. First go to this directory:cd speptide
 324 <P>
 325 To be able to simulate the S-Peptide we need a starting structure. This can
 326 be taken from the protein data bank. There are a number of different
 327 structure for Ribonuclease S, from one of which we have cut out the
 328 first 20 residues, and stored it in
 329 <TT><a href="pdb.html">speptide.pdb</a></TT>.
 330 Have a look at the file
 331 <PRE>
 332 % more <a href="pdb.html">speptide.pdb</a>
 333 </PRE>
 334 If you have access to a molecular
 335 graphics program such as rasmol, xmol,
 336 or a commercial package,
 337 you can look at the molecule on screen, eg:
 338 <PRE>
 339 % rasmol <a href="pdb.html">speptide.pdb</a>
 340 </PRE>
 341
 342 The following steps have to be taken to perform a simulation of the peptide.
 343 <ol>
 344 <li>    Convert the pdb-file <a href="pdb.html">speptide.pdb</a>
 345         to a GROMACS structure file and a GROMACS topology file.
 346 <li>    Solvate the peptide in water
 347 <li>    Perform an energy minimization of the peptide in solvent
 348 <li>    Add ions if necessary (we will omit this step here)
 349 <li>    Perform a short MD run with position restraints on the peptide
 350 <li>    Perform full MD without restraints
 351 <li>    Analysis
 352 </ol>
 353
 354 We will describe in detail how such a simulation can be done,
 355 starting from a pdb-file.
 356
 357 <P><H3><A NAME="pdb2gmx">
 358 Generate a topology file (<tt><a href="top.html">.top</a></tt>) from the pdb-file (<tt><a href="pdb.html">.pdb</a></TT>)</a>
 359 </H3>
 360 <P>
 361 Generate a molecular topology and a structure file in
 362 format. This can be done with the <a href="pdb2gmx.html">pdb2gmx</a> program:
 363 <PRE>
 364 % <a href="pdb2gmx.html">pdb2gmx</a> -f <a href="pdb.html">speptide.pdb</a> -p <a href="top.html">speptide.top</a> -o <a href="gro.html">speptide.gro</a>
 365 </PRE>
 366 Note that the correct file extension are added automatically to the
 367 filenames on the command line.
 368 You will only be asked to choose a forcefield, choose 0, but you can also
 369 have <a href="pdb2gmx.html">pdb2gmx</a> ask you
 370 about protonation of residues, and about protonation of N- and C-terminus.
 371 You can type
 372 <PRE>
 373 % <a href="pdb2gmx.html">pdb2gmx</a> -h
 374 </PRE>
 375 to see the available options.
 376 <P>
 377 The <a href="pdb2gmx.html">
 378 pdb2gmx</a> program has generated a topology file
 379 <TT><a href="top.html">speptide.top</a></TT> and a
 380 GROMACS structure file <tt><a href="gro.html">speptide.gro</a></tt> and it will
 381 generate hydrogen
 382 positions. The <tt>-p</tt> and <tt>-o</tt> options with he
 383 filenames are optional; without them the files <TT><a href="top.html">topol.top</a></TT> and <TT>
 384 <a href="gro.html">conf.gro</a></TT> will be generated.
 385 Now have a look at the output from <a href="pdb2gmx.html">pdb2gmx</a>,
 386 <PRE>
 387 % more <a href="gro.html">speptide.gro</a>
 388 </PRE>
 389 You will see a close resemblance to the <a href="pdb.html">pdb</a> file, only the layout of
 390 the file is a bit different.
 391 Also do have a look at the topology
 392 <PRE>
 393 % more <a href="top.html">speptide.top</a>
 394 </PRE>
 395 You will see a large file containing the atom types, the physical
 396 bonds between atoms, etcetera.
 397
 398 <P><H3><A NAME="solvate">
 399 Solvate the peptide in a periodic box filled with water</A></H3>
 400 This is done using the programs
 401 <a href="editconf.html">editconf</a> and
 402 <a href="genbox.html">genbox</a>.
 403 <a href="editconf.html">editconf</a>
 404 will make a rectangular box with empty space of user specified size
 405 around the molecule.
 406 <a href="genbox.html">genbox</a>
 407 will read the structure file and fill the box with water.
 408 <PRE>
 409 % <a href="editconf.html">editconf</a> -f speptide -o -dc 0.5<BR>
 410 % <a href="genbox.html">genbox</a> -cp out -cs -p speptide -o b4em
 411 </PRE>
 412 The program prints some lines of user information, like the volume of
 413 the box and the number of water molecules added to your
 414 peptide. <TT><a href="genbox.html">genbox</a></TT>
 415 also changes the topology file
 416 <TT><a href="top.html">speptide.top</a></TT> to include
 417 these water molecules in the topology. This can been seen by looking
 418 at the bottom of the
 419 <TT><a href="top.html">speptide.top</a></TT> file
 420 <PRE>
 421 % tail <a href="top.html">speptide.top</a>
 422 </PRE>
 423 You will see some lines like
 424 <PRE>
 425 [ system ]
 426 ; Name          Number
 427 Protein         1
 428 SOL             N
 429 </PRE>
 430 where <tt>N</tt> is the number of water molecules added to your system by
 431 <TT><a href="genbox.html">genbox</a></TT>.
 432 <P>
 433
 434 It is also possible to solvate a peptide in another solvent such as
 435 dimethylsulfoxide (DMSO), as has been done by
 436 <A HREF=#mierke91>Mierke & Kessler, 1991</A>.
 437
 438 <P><H3><A NAME="indexfile">Generate index file (<TT><a href="ndx.html">.ndx</a></TT> extension)</A></H3>
 439 By default, most GROMACS programs generate a set of index groups to select
 440 the most common subsets of atoms from your system (e.g. Protein, Backbone,
 441 C-alpha's, Solute, etc.).
 442 For the special cases when you need to select other groups than the
 443 default ones, an <a href="ndx.html">index file</a>
 444 can be generated using <a href="make_ndx.html">make_ndx</a>.
 445 This is an interactive program that lets you manipulate molecules,
 446 residues and atom. It's use should be self-explanatory.  To invoke the
 447 program you would
 448 <PRE>
 449 % <a href="make_ndx.html">make_ndx</a> -f b4em
 450 </PRE>
 451 but don't bother for now.
 452
 453 <P><H3><A NAME="em">Perform an energy minimization of the peptide in solvent</A></H3>
 454
 455 Now we have to perform an <EM>energy minimization</EM> of the
 456 structure to remove the local strain in the peptide (due to generation
 457 of hydrogen positions) and to remove bad Van der Waals contacts
 458 (particles that are too close). This can be done with the
 459 <TT><a href="mdrun.html">mdrun</a></TT> program which
 460 is the MD and EM program. Before we can use the
 461 <TT> <a href="mdrun.html">mdrun</a></TT> program
 462 however, we have to preprocess the topology file (
 463 <TT><a href="top.html">speptide.top</a></TT>), the
 464 structure file (
 465 <TT><a href="gro.html">speptide.gro</a></TT>) and a
 466 special parameter file (<TT><a href="mdp_opt.html">em.mdp</a></TT>). Check
 467 the contents of this file
 468 <PRE>
 469 % more <a href="mdp_opt.html">em.mdp</a>
 470 </PRE>
 471 Preprocessing is done with the preprocessor called
 472 <TT><a href="grompp.html">grompp</a></TT>. This reads
 473 up the files just mentioned:
 474
 475 <PRE>
 476 % <a href="grompp.html">grompp</a> -v -f em -c b4em -o em -p speptide
 477 </PRE>
 478 In this command the <tt>-v</tt> option turns on verbose mode, which
 479 gives a little bit of clarifying info on what the program is doing.
 480 We now have made a <EM>run input file</EM> (<TT><a href="tpr.html">em.tpr</a></TT>) which
 481 serves as input for the
 482 <TT><a href="mdrun.html">mdrun</a></TT> program. Now
 483 we can do the energy minimization:
 484 <PRE>
 485 % <a href="mdrun.html">mdrun</a> -v -s em -o em -c after_em -g emlog
 486 </PRE>
 487 In this command the <tt>-v</tt> option turns on verbose mode again.
 488 The <tt>-o</tt> option sets the filename for the trajectory file,
 489 which is not very important in energy minimizations. The <tt>-c</tt>
 490 option sets the filename of the structure file after energy
 491 minimization. This file we will subsequently use as input for the MD
 492 run.  The energy minimization takes some time, the amount depending on
 493 the CPU in your computer, the load of your computer, etc. The
 494 <TT><a href="mdrun.html">mdrun</a></TT> program is
 495 automatically <EM>niced</EM>; it runs at low priority. All programs
 496 that do extensive computations are automatically run at low
 497 priority. For most modern workstations this computation should be a
 498 matter of minutes. The minimization is finished when either the
 499 minimization has converged or a fixed number of steps has been
 500 performed.  Since the system consists merely of water, a quick check
 501 on the potential energy should reveal whether the minimization was
 502 successful: the potential energy of 1 SPC water molecule at 300 K is
 503 <tt>-42</tt> kJ mole<sup>-1</sup>. Since we have about <tt>2.55e+03</tt>
 504 SPC molecules the potential energy should be about <tt>-1.1e+5</tt> kJ
 505 mol<sup>-1</sup>. If the potential energy after minimization is lower
 506 than <tt>-1.1e+05</tt> kJ mol<sup>-1</sup> it is acceptable and the
 507 structure can be used for MD calculations.  After our EM calculation
 508 the program prints something like:
 509 <PRE>
 510 STEEPEST DESCENTS converged to 2000
 511   Potential Energy  = -1.19482e+05
 512 </PRE>
 513 which means our criterium is met, and we can proceed to the next step.
 514
 515 <P><H3><A NAME="posres">
 516 Perform a short MD run with position restraints on the peptide</A>
 517 </H3>
 518 Position restrained MD means Molecular Dynamics in which a part of the
 519 system is not allowed to move far off their starting positions.  To be
 520 able to run with position restraints we must add a section to the
 521 <TT><a href="top.html">speptide.top</a></TT> file,
 522 describing which atoms are to be restrained. Such a section is
 523 actually generated by the
 524 <a href="pdb2gmx.html">pdb2gmx</a> program. In the
 525 topology file it looks like
 526 <PRE>
 527 #ifdef POSRES<BR>
 528 #include "<a href="itp.html">posres.itp</a>"<BR>
 529 #endif
 530 </PRE>
 531 In the <a href="top.html">topology file</a> we use
 532 conditional inclusion, i.e. only if a variable <TT>POSRES</TT> is set
 533 in the preprocessor do we include the file, this allows us to use the
 534 same topology file for runs with and without position restraints. In
 535 the <a href="mdp_opt.html"><TT>pr.mdp</TT></a> parameter file
 536 for the position restraints this variable is set indeed:
 537 <PRE>
 538 define              =  -DPOSRES
 539 </PRE>
 540 <P>
 541 At last we can generate the input for the position restrained mdrun:
 542 <PRE>
 543 % <a href="grompp.html">grompp</a> -f pr -o pr -c after_em -r after_em -p speptide
 544 </PRE>
 545 Now it's <a href="mdrun.html">MDrun</a> time:
 546 <PRE>
 547 % <a href="mdrun.html">mdrun</a> -v -s pr -e pr -o pr -c after_pr -g prlog >& pr.job &
 548 </PRE>
 549 This run is started in the background (it will take a while), you
 550 can watch how long it will take by typing:
 551 <PRE>
 552 % tail -f pr.job
 553 </PRE>
 554 With the <tt>Ctrl-C</tt> key you can kill the <tt>tail</tt> command.
 555 A good check of your simulation is to see whether density and potential
 556 energies have converged:
 557 <PRE>
 558 % <a href="g_energy.html">g_energy</a> -f pr -o out -w
 559 </PRE>
 560 The <a href="g_energy.html">
 561 g_energy</a> program will prompt you to select a number of energy terms
 562 from a list. For potential energy type:
 563 <PRE>
 564 9 0
 565 </PRE>
 566 If you have the xmgr program installed it will automatically pop up on your
 567 screen with the energy plot. You can do the same for the density
 568 and other energy terms, such as Solvent-Protein interactions.
 569
 570 <P><H3><A NAME="full">Perform full MD without restraints</A></H3>
 571 Full MD is very similar to the restrained MD as far as GROMACS is
 572 concerned. Check out the <TT><a href="mdp_opt.html">full.mdp</a></TT> for details.
 573 <PRE>
 574 % <a href="grompp.html">grompp</a> -v -f full -o full -c after_pr -p speptide
 575 </PRE>
 576 Then we can start mdrunning
 577 <PRE>
 578 % <a href="mdrun.html">mdrun</a> -v -s full -e full -o full -c after_full -g flog >& full.job &
 579 </PRE>
 580 You should do similar convergence checks (and more!) as for the position
 581 restrained simulation.
 582
 583 <P><H3><A NAME="analysis">Analysis</A></H3>
 584 We will not describe analysis in detail, because most analysis tools
 585 are described in the Analysis chapter of the printed manual.
 586 We just list a few of the possibilities within GROMACS. By now you should be
 587 able to start programs yourself.
 588 <P><UL>
 589 <LI> View the trajectory on your own X-screen (program
 590 <a href="ngmx.html">ngmx</a>).
 591 <li> Monitor energies using
 592         <a href="g_energy.html">g_energy</a>.
 593
 594 <li> Root Mean Square Deviation with respect to the crystal
 595         structure (program
 596         <a href="g_rms.html">g_rms</a>).
 597 <LI> Radius of Gyration (program
 598         <a href="g_gyrate.html">g_gyrate</a>).  ).
 599 <LI> Secondary Structure analysis (program
 600         <a href="do_dssp.html">do_dssp</a>).
 601         For this analysis you should have the dssp
 602         (<A HREF=#kabsch83>Kabsch & Sander, 1983</A>)
 603         software installed. This program also produces
 604         the solvent accesible surface area as a function of time.
 605 <LI> Ramachandran Plots (program
 606         <a href="g_rama.html">g_rama</a>).
 607 <LI> Salt Bridge analysis (program
 608         <a href="g_saltbr.html">g_saltbr</a>).
 609 </ul>
 610 <P>
 611 You have been witness of a full MD simulation starting from a pdb-file.
 612 It's that easy, but then again, maybe it was not that easy. The
 613 example presented here is a <EM>real</EM> example, this is how a
 614 production run should be performed, the complexity is in the process
 615 itself and not in the software (at least, that's our opinion).</p>
 616
 617 <br><hr><br>
 618
 619 <P><H1><A NAME="you">Your own System.</A></H1>
 620 <P>
 621 For proteins in water (or other solvent) the route is described above.
 622 For other systemd (eg. pure liquids or mixtures) one needs:
 623 <ul>
 624 <li>    The atomic coordinates, which can be generated by a variety of
 625         interactive programs (eg. Quanta, Cerius, HyperChem).
 626         Coordinate files can be exported in pdb-format and
 627         converted to <TT><a href="gro.html">.gro</a></TT> format by
 628         the <a href="editconf.html">editconf</a> program:
 629         <PRE>
 630 % <a href="editconf.html">editconf</a> -f <a href="pdb.html">conf.pdb</a> -o <a href="gro.html">conf.gro</a>
 631         </PRE>
 632         where <TT><a href="gro.html">conf.gro</a></TT> is the  coordinatefile,
 633         or converted back to pdb-format by
 634         <PRE>
 635 % <a href="editconf.html">editconf</a> -f <a href="gro.html">conf.gro</a> -o <a href="pdb.html">conf.pdb</a>
 636         </PRE>
 637         where <TT>conf</TT> is a file with  coordinates, and <TT>
 638         <a href="pdb.html">conf.pdb</a></TT> is the target file in <tt><a href="pdb.html">.pdb</a></tt> format.
 639         <b>NOTE:</b> Make sure that the graphics programs export
 640         <b>whole</b> molecules instead of molecules that are cut in pieces
 641         (due to the periodic boundary conditions)
 642         If you have the coordinates of single molecules, you can also
 643         build systems (pure liquids or mixtures) with
 644         <a href="genbox.html">genbox</a>.
 645         In contrast, the program
 646         <a href="genconf.html">genconf</a>
 647         produces the lattice of molecules with random displacements.
 648 <li>    The topology you have to build yourself. Of course you can
 649         include topologies of part of your system (eg. <TT><a href="itp.html">spc.itp</a></TT>,
 650         <TT><a href="itp.html">decane.itp</a></TT> etc.)
 651 </ul>
 652 <br><hr><br>
 653
 654 <P><H1><A NAME="info">More Info</A></h1>
 655
 656 <P>
 657 More info can be found in the
 658 <A HREF="flow.html">flowchart</A>
 659 (for a quick overview) and the
 660 <A HREF="../gmxfaq.html">GMX FAQ</A>.
 661 </P>
 662
 663 <br><hr><br>
 664
 665 <P><H1><A NAME="ref">References</A></h1>
 666
 667 <blockquote>
 668 <dl>
 669
 670 <dt><A NAME="berendsen81">Berendsen, H.J.C., Postma, J.P.M., van
 671 Gunsteren, W.F., Hermans, J. (1981) <dd><it>Intermolecular
 672 Forces</it>, chapter Interaction models for water in relation to
 673 protein hydration, pp 331-342. Dordrecht: D. Reidel Publishing Company
 674 Dordrecht</dd><p>
 675
 676 <dt><A NAME="kabsch83">Kabsch, W., Sander, C. (1983). <dd>Dictionary
 677 of protein secondary structure: Pattern recognition of hydrogen-bonded
 678 and geometrical features. <it>Biopolymers</it> <b>22</b>,
 679 2577--2637.</dd><p>
 680
 681 <dt><A NAME="mierke91">Mierke, D.F., Kessler, H. (1991). <dd>Molecular
 682 dynamics with dimethyl sulfoxide as a solvent. Conformation of a
 683 cyclic hexapeptide. <it>J. Am. Chem. Soc.</it> <b>113</b>, 9446.</dd><p>
 684
 685 <dt><A NAME="stryer88">Stryer, L. (1988). <dd><it>Biochemistry</it>
 686 vol. 1, p. 211. New York: Freeman, 3 edition.</dd><p>
 687
 688 </dl>
 689 </blockquote>
 690
 691 <br><hr><br>
 692 </BODY>
 693 </HTML>