Small fixes in mdrun desc.; enable periodic molecules

diff --git a/src/kernel/mdrun.c b/src/kernel/mdrun.c
index 7d1759c5af4df6e29618ce641ddc03870abdb36a..8ea8c82a851109f4c1e8e94ad7e3aa64f663f0e6 100644 (file)
--- a/src/kernel/mdrun.c
+++ b/src/kernel/mdrun.c
@@ -64,17 +64,6 @@ int main(int argc,char *argv[])
        "This release is targeted at developers and advanced users and",
        "should not be considered ready for production. The following should be",
        "noted before using the program:[PAR]",
-       "Usage:[BR]",
-       "$ mdrun -device \"OpenMM:platform=Cuda,memtest=15,deviceid=0,force-device=no\"[PAR]",
-       "OpenMM options:[PAR]",
-       "      [TT]platform[tt] = Cuda\nThe only available value. OpenCL support will be available soon[PAR]",
-       "      [TT]memtest[tt] = 15\nRun a partial, random GPU memory test for the given amount of seconds. A full test",
-       "(recommended!) can be run with \"full\". Memory testing can be disabled with \"off\".[PAR]",
-       "      [TT]deviceid[tt] = 0\nSpecify the target device when multiple cards are present.",
-       "Only one card can be used at any given time though.[PAR]",
-       "      [TT]force-device[tt] = no\nIf set to \"yes\" mdrun  will be forced to execute on",
-       "hardware that is not officially supported. GPU acceleration can also be achieved on older,",
-       "but Cuda capable, cards although the simulation might be too slow, and the memory limits too strict.[PAR]",
        " * The current release runs only on modern nVidia GPU hardware with CUDA support.",
        "Make sure that the necessary CUDA drivers and libraries for your operating system",
        "are already installed. The CUDA SDK also should be installed in order to compile",
@@ -126,7 +115,19 @@ int main(int argc,char *argv[])
     "The energy file ([TT]-e[tt]) contains energies, the temperature,",
     "pressure, etc, a lot of these things are also printed in the log file.",
     "Optionally coordinates can be written to a compressed trajectory file",
-    "([TT]-x[tt]).",
+    "([TT]-x[tt]).[PAR]",
+//////////////////////////////////////
+       "Usage with OpenMM:[BR]",
+       "$ mdrun -device \"OpenMM:platform=Cuda,memtest=15,deviceid=0,force-device=no\"[PAR]",
+       "Options:[PAR]",
+       "      [TT]platform[tt] = Cuda\t\t:\tThe only available value. OpenCL support will be available in future.\n",
+       "      [TT]memtest[tt] = 15\t\t:\tRun a partial, random GPU memory test for the given amount of seconds. A full test",
+       "(recommended!) can be run with \"memtest=full\". Memory testing can be disabled with \"memtest=off\".\n",
+       "      [TT]deviceid[tt] = 0\t\t:\tSpecify the target device when multiple cards are present.",
+       "Only one card can be used at any given time though.\n",
+       "      [TT]force-device[tt] = no\t\t:\tIf set to \"yes\" mdrun  will be forced to execute on",
+       "hardware that is not officially supported. GPU acceleration can also be achieved on older",
+       "but Cuda capable cards, although the simulation might be too slow, and the memory limits too strict.",
 #else
     "The mdrun program is the main computational chemistry engine",
     "within GROMACS. Obviously, it performs Molecular Dynamics simulations,",
@@ -336,6 +337,11 @@ int main(int argc,char *argv[])
     { efSTO, "-c",      "confout",  ffWRITE },
     { efEDR, "-e",      "ener",     ffWRITE },
     { efLOG, "-g",      "md",       ffWRITE },
+    { efEDI, "-ei",     "sam",      ffOPTRD },
+    { efTRX, "-rerun",  "rerun",    ffOPTRD },
+    { efXVG, "-table",  "table",    ffOPTRD },
+    { efXVG, "-tablep", "tablep",   ffOPTRD },
+    { efXVG, "-tableb", "table",    ffOPTRD },
 #ifndef GMX_OPENMM
     { efXVG, "-dhdl",   "dhdl",     ffOPTWR },
     { efXVG, "-field",  "field",    ffOPTWR },

diff --git a/src/kernel/openmm_wrapper.cpp b/src/kernel/openmm_wrapper.cpp
index 9ca3a2ca376e336a0c45d7f1b6e747abd98282a2..20cd9a995f4f50dd435e77fbb4e1289038f9bfd4 100644 (file)
--- a/src/kernel/openmm_wrapper.cpp
+++ b/src/kernel/openmm_wrapper.cpp
@@ -333,10 +333,6 @@ void checkGmxOptions(t_inputrec *ir, gmx_localtop_t *top)
             "Use NoCutoff (i.e. rcoulomb = rvdw = 0 ),Reaction-Field, Ewald or PME.\n");
     }
 
-    /* TODO what is this code checking? */
-    if (ir->bPeriodicMols)
-        gmx_fatal(FARGS,"** OpenMM Error ** : Systems with periodic molecules ares not supported\n");
-
     if ( (ir->etc != etcNO) && (ir->etc != etcANDERSEN) && (ir->etc != etcANDERSENINTERVAL))
         gmx_fatal(FARGS,"** OpenMM Error ** : Temperature coupling can be achieved by "
                 "using either \n\t(1)\t\"md-vv\" or \"md-vvak\" integrators with \"andersen\" or "