Add hack to fix genbox

Using a lighter-weight neighbour search is a better idea, but this bug
needs fixing right now.

Add integration tests for major functionality of genbox. These pass
only with the fix in this patch. These are not the most glorious
tests, but as demonstrated by this bug, "does not segfault in routine
workflows" is useful.

Fixes #1393

Change-Id: I5628f52cd91dcb64d66e690b2e611e524f450972

diff --git a/src/gromacs/gmxpreprocess/CMakeLists.txt b/src/gromacs/gmxpreprocess/CMakeLists.txt
index 272b111fc29c45e89801ee6b69e86c8fe961bf04..dc51659f4da8806cb6505d036850b02b2d4b700f 100644 (file)
--- a/src/gromacs/gmxpreprocess/CMakeLists.txt
+++ b/src/gromacs/gmxpreprocess/CMakeLists.txt
@@ -1,7 +1,7 @@
 #
 # This file is part of the GROMACS molecular simulation package.
 #
-# Copyright (c) 2011,2013, by the GROMACS development team, led by
+# Copyright (c) 2011,2013,2014, by the GROMACS development team, led by
 # Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
 # and including many others, as listed in the AUTHORS file in the
 # top-level source directory and at http://www.gromacs.org.
@@ -35,3 +35,7 @@
 file(GLOB GMXPREPROCESS_SOURCES *.c *.cpp)
 
 set(LIBGROMACS_SOURCES ${LIBGROMACS_SOURCES} ${GMXPREPROCESS_SOURCES} PARENT_SCOPE)
+
+if(BUILD_TESTING)
+    add_subdirectory(tests)
+endif(BUILD_TESTING)

diff --git a/src/gromacs/gmxpreprocess/genbox-addconf.c b/src/gromacs/gmxpreprocess/genbox-addconf.c
index 9eb2f1ca448583351c0a11f17a2a084baf659444..e5c65836fca4b3ecb84c431881bc7f20f8266e87 100644 (file)
--- a/src/gromacs/gmxpreprocess/genbox-addconf.c
+++ b/src/gromacs/gmxpreprocess/genbox-addconf.c
@@ -254,10 +254,11 @@ static void do_nsgrid(FILE *fp, gmx_bool bVerbose,
 
     /* inputrec structure */
     snew(ir, 1);
-    ir->coulombtype = eelCUT;
-    ir->vdwtype     = evdwCUT;
-    ir->ndelta      = 2;
-    ir->ns_type     = ensGRID;
+    ir->cutoff_scheme = ecutsGROUP;
+    ir->coulombtype   = eelCUT;
+    ir->vdwtype       = evdwCUT;
+    ir->ndelta        = 2;
+    ir->ns_type       = ensGRID;
     snew(ir->opts.egp_flags, 1);
 
     top = gmx_mtop_generate_local_top(mtop, ir);

diff --git a/src/gromacs/gmxpreprocess/genbox.cpp b/src/gromacs/gmxpreprocess/genbox.cpp
index 4c5264115080983ce0c7b19da1ec6d6af5c136a1..f1b9bafd057f046abf612a72ef30078b6b212ef5 100644 (file)
--- a/src/gromacs/gmxpreprocess/genbox.cpp
+++ b/src/gromacs/gmxpreprocess/genbox.cpp
@@ -1002,7 +1002,7 @@ int gmx_genbox(int argc, char *argv[])
     const char     *enum_rot_string[] = {NULL, "xyz", "z", "none", NULL};
     t_pargs         pa[]              = {
         { "-box",    FALSE, etRVEC, {new_box},
-          "Box size" },
+          "Box size (in nm)" },
         { "-nmol",   FALSE, etINT, {&nmol_ins},
           "Number of extra molecules to insert" },
         { "-try",    FALSE, etINT, {&nmol_try},

diff --git a/src/gromacs/gmxpreprocess/tests/CMakeLists.txt b/src/gromacs/gmxpreprocess/tests/CMakeLists.txt
new file mode 100644 (file)
index 0000000..a990ab7
--- /dev/null
+++ b/src/gromacs/gmxpreprocess/tests/CMakeLists.txt
@@ -0,0 +1,49 @@
+#
+# This file is part of the GROMACS molecular simulation package.
+#
+# Copyright (c) 2014, by the GROMACS development team, led by
+# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+# and including many others, as listed in the AUTHORS file in the
+# top-level source directory and at http://www.gromacs.org.
+#
+# GROMACS is free software; you can redistribute it and/or
+# modify it under the terms of the GNU Lesser General Public License
+# as published by the Free Software Foundation; either version 2.1
+# of the License, or (at your option) any later version.
+#
+# GROMACS is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+# Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with GROMACS; if not, see
+# http://www.gnu.org/licenses, or write to the Free Software Foundation,
+# Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
+#
+# If you want to redistribute modifications to GROMACS, please
+# consider that scientific software is very special. Version
+# control is crucial - bugs must be traceable. We will be happy to
+# consider code for inclusion in the official distribution, but
+# derived work must not be called official GROMACS. Details are found
+# in the README & COPYING files - if they are missing, get the
+# official version at http://www.gromacs.org.
+#
+# To help us fund GROMACS development, we humbly ask that you cite
+# the research papers on the package. Check out http://www.gromacs.org.
+
+set(testname "PreprocessingTests")
+set(exename "preprocessing-tools-test")
+
+#include_directories(${CMAKE_SOURCE_DIR}/src/gromacs/gmxpreprocess)
+
+gmx_build_unit_test(
+    ${testname}
+    ${exename}
+    # files with code for test fixtures
+    genbox.cpp
+    )
+gmx_register_integration_test(
+    ${testname}
+    ${exename}
+    )

diff --git a/src/gromacs/gmxpreprocess/tests/genbox.cpp b/src/gromacs/gmxpreprocess/tests/genbox.cpp
new file mode 100644 (file)
index 0000000..00032a8
--- /dev/null
+++ b/src/gromacs/gmxpreprocess/tests/genbox.cpp
@@ -0,0 +1,119 @@
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \internal \file
+ * \brief
+ * Tests for gmx traj
+ *
+ * \author Mark Abraham <mark.j.abraham@gmail.com>
+ */
+
+#include "../genbox.h"
+#include "testutils/integrationtests.h"
+#include "testutils/cmdlinetest.h"
+#include "gromacs/fileio/futil.h"
+
+namespace
+{
+
+//! Test fixture for genbox
+class Genbox : public gmx::test::IntegrationTestFixture
+{
+    public:
+        //! Constructor
+        Genbox()
+            : cpFileName(fileManager_.getInputFilePath("spc-and-methanol.gro")),
+              ciFileName(fileManager_.getInputFilePath("x.gro")),
+              topFileName(fileManager_.getInputFilePath("spc-and-methanol.top")),
+              outputFileName(fileManager_.getTemporaryFilePath("out.gro"))
+        {
+            caller.append("genbox");
+            caller.addOption("-o", outputFileName);
+        }
+
+    public:
+        //! Name of file to use for -cp
+        std::string            cpFileName;
+        //! Name of file to use for -ci
+        std::string            ciFileName;
+        //! Name of input file to use for -p (if used)
+        std::string            topFileName;
+        //! Name of output file to use for -o
+        std::string            outputFileName;
+        //! Helper object for managing the call to gmx_genbox
+        gmx::test::CommandLine caller;
+};
+
+TEST_F(Genbox, cs_box_Works)
+{
+    caller.append("-cs"); // use default solvent box
+    caller.addOption("-box", "1.1");
+
+    ASSERT_EQ(0, gmx_genbox(caller.argc(), caller.argv()));
+}
+
+TEST_F(Genbox, cs_cp_Works)
+{
+    caller.append("-cs"); // use default solvent box
+    caller.addOption("-cp", cpFileName);
+
+    ASSERT_EQ(0, gmx_genbox(caller.argc(), caller.argv()));
+}
+
+TEST_F(Genbox, cs_cp_p_Works)
+{
+    caller.append("-cs"); // use default solvent box
+    caller.addOption("-cp", cpFileName);
+
+    std::string modifiableTopFileName = fileManager_.getTemporaryFilePath(".top");
+    gmx_file_copy(topFileName.c_str(), modifiableTopFileName.c_str(), true);
+    caller.addOption("-p", modifiableTopFileName);
+
+    ASSERT_EQ(0, gmx_genbox(caller.argc(), caller.argv()));
+}
+
+TEST_F(Genbox, ci_Works)
+{
+    caller.addOption("-cp", fileManager_.getInputFilePath("spc216.gro"));
+    caller.addOption("-nmol", "2");
+    caller.addOption("-ci", ciFileName);
+    caller.addOption("-vdwd", "0.01"); // Make sure insertions happen
+
+    ASSERT_EQ(0, gmx_genbox(caller.argc(), caller.argv()));
+}
+
+// TODO Someone who knows what -ip is good for should write something
+// to test it
+
+} // namespace

diff --git a/src/gromacs/gmxpreprocess/tests/spc-and-methanol.gro b/src/gromacs/gmxpreprocess/tests/spc-and-methanol.gro
new file mode 100644 (file)
index 0000000..4e937af
--- /dev/null
+++ b/src/gromacs/gmxpreprocess/tests/spc-and-methanol.gro
@@ -0,0 +1,9 @@
+
+ 6
+    1MeOH   Me1    1   1.970   1.460   1.209 -0.8587 -0.1344 -0.0643
+    1MeOH    O2    2   1.978   1.415   1.082  0.0623 -0.1787  0.0036
+    1MeOH    H3    3   1.905   1.460   1.030 -0.5020 -0.9564  0.0997
+    2SOL     OW    4   1.555   1.511   0.703   0.869   1.245   1.665
+    2SOL    HW1    5   1.498   1.495   0.784   0.169   0.275   1.565
+    2SOL    HW2    6   1.496   1.521   0.623   0.269   2.275   1.465
+   3.01000   3.01000   3.01000

diff --git a/src/gromacs/gmxpreprocess/tests/spc-and-methanol.top b/src/gromacs/gmxpreprocess/tests/spc-and-methanol.top
new file mode 100644 (file)
index 0000000..7f78ad6
--- /dev/null
+++ b/src/gromacs/gmxpreprocess/tests/spc-and-methanol.top
@@ -0,0 +1,12 @@
+#include "gromos43a1.ff/forcefield.itp"
+#include "gromos43a1.ff/methanol.itp"
+#include "gromos43a1.ff/spc.itp"
+
+[ system ]
+; Name
+spc-and-methanol
+
+[ molecules ]
+; Compound  #mols
+Methanol    1
+SOL         1

diff --git a/src/gromacs/gmxpreprocess/tests/spc216.gro b/src/gromacs/gmxpreprocess/tests/spc216.gro
new file mode 100644 (file)
index 0000000..49449af
--- /dev/null
+++ b/src/gromacs/gmxpreprocess/tests/spc216.gro
@@ -0,0 +1,651 @@
+216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984
+  648
+    1SOL     OW    1    .230    .628    .113
+    1SOL    HW1    2    .137    .626    .150
+    1SOL    HW2    3    .231    .589    .021
+    2SOL     OW    4    .225    .275   -.866
+    2SOL    HW1    5    .260    .258   -.774
+    2SOL    HW2    6    .137    .230   -.878
+    3SOL     OW    7    .019    .368    .647
+    3SOL    HW1    8   -.063    .411    .686
+    3SOL    HW2    9   -.009    .295    .584
+    4SOL     OW   10    .569   -.587   -.697
+    4SOL    HW1   11    .476   -.594   -.734
+    4SOL    HW2   12    .580   -.498   -.653
+    5SOL     OW   13   -.307   -.351    .703
+    5SOL    HW1   14   -.364   -.367    .784
+    5SOL    HW2   15   -.366   -.341    .623
+    6SOL     OW   16   -.119    .618    .856
+    6SOL    HW1   17   -.086    .712    .856
+    6SOL    HW2   18   -.068    .564    .922
+    7SOL     OW   19   -.727    .703    .717
+    7SOL    HW1   20   -.670    .781    .692
+    7SOL    HW2   21   -.787    .729    .793
+    8SOL     OW   22   -.107    .607    .231
+    8SOL    HW1   23   -.119    .594    .132
+    8SOL    HW2   24   -.137    .526    .280
+    9SOL     OW   25    .768   -.718   -.839
+    9SOL    HW1   26    .690   -.701   -.779
+    9SOL    HW2   27    .802   -.631   -.875
+   10SOL     OW   28    .850    .798   -.039
+   10SOL    HW1   29    .846    .874    .026
+   10SOL    HW2   30    .872    .834   -.130
+   11SOL     OW   31    .685   -.850    .665
+   11SOL    HW1   32    .754   -.866    .735
+   11SOL    HW2   33    .612   -.793    .703
+   12SOL     OW   34    .686   -.701   -.059
+   12SOL    HW1   35    .746   -.622   -.045
+   12SOL    HW2   36    .600   -.670   -.100
+   13SOL     OW   37    .335   -.427   -.801
+   13SOL    HW1   38    .257   -.458   -.854
+   13SOL    HW2   39    .393   -.369   -.858
+   14SOL     OW   40   -.402   -.357   -.523
+   14SOL    HW1   41   -.378   -.263   -.497
+   14SOL    HW2   42   -.418   -.411   -.441
+   15SOL     OW   43    .438    .392   -.363
+   15SOL    HW1   44    .520    .336   -.354
+   15SOL    HW2   45    .357    .334   -.359
+   16SOL     OW   46   -.259    .447    .737
+   16SOL    HW1   47   -.333    .493    .687
+   16SOL    HW2   48   -.208    .515    .790
+   17SOL     OW   49    .231   -.149    .483
+   17SOL    HW1   50    .265   -.072    .537
+   17SOL    HW2   51    .275   -.149    .393
+   18SOL     OW   52   -.735   -.521   -.172
+   18SOL    HW1   53   -.688   -.521   -.084
+   18SOL    HW2   54   -.783   -.608   -.183
+   19SOL     OW   55    .230   -.428    .538
+   19SOL    HW1   56    .204   -.332    .538
+   19SOL    HW2   57    .159   -.482    .583
+   20SOL     OW   58    .240   -.771    .886
+   20SOL    HW1   59    .254   -.855    .938
+   20SOL    HW2   60    .185   -.707    .941
+   21SOL     OW   61    .620   -.076   -.423
+   21SOL    HW1   62    .528   -.093   -.388
+   21SOL    HW2   63    .648    .016   -.397
+   22SOL     OW   64    .606   -.898    .123
+   22SOL    HW1   65    .613   -.814    .069
+   22SOL    HW2   66    .652   -.885    .211
+   23SOL     OW   67   -.268    .114   -.382
+   23SOL    HW1   68   -.286    .181   -.454
+   23SOL    HW2   69   -.271    .160   -.293
+   24SOL     OW   70    .122    .643    .563
+   24SOL    HW1   71    .077    .555    .580
+   24SOL    HW2   72    .121    .697    .647
+   25SOL     OW   73   -.020   -.095    .359
+   25SOL    HW1   74    .034   -.124    .439
+   25SOL    HW2   75    .010   -.005    .330
+   26SOL     OW   76    .027   -.266    .117
+   26SOL    HW1   77    .008   -.362    .138
+   26SOL    HW2   78   -.006   -.208    .192
+   27SOL     OW   79   -.173    .922    .612
+   27SOL    HW1   80   -.078    .893    .620
+   27SOL    HW2   81   -.181    .987    .537
+   28SOL     OW   82   -.221   -.754    .432
+   28SOL    HW1   83   -.135   -.752    .380
+   28SOL    HW2   84   -.207   -.707    .520
+   29SOL     OW   85    .113    .737   -.265
+   29SOL    HW1   86    .201    .724   -.220
+   29SOL    HW2   87    .100    .834   -.287
+   30SOL     OW   88    .613   -.497    .726
+   30SOL    HW1   89    .564   -.584    .735
+   30SOL    HW2   90    .590   -.454    .639
+   31SOL     OW   91   -.569   -.634   -.439
+   31SOL    HW1   92   -.532   -.707   -.497
+   31SOL    HW2   93   -.517   -.629   -.354
+   32SOL     OW   94    .809    .004    .502
+   32SOL    HW1   95    .849    .095    .493
+   32SOL    HW2   96    .709    .012    .508
+   33SOL     OW   97    .197   -.886   -.598
+   33SOL    HW1   98    .286   -.931   -.612
+   33SOL    HW2   99    .124   -.951   -.617
+   34SOL     OW  100   -.337   -.863    .190
+   34SOL    HW1  101   -.400   -.939    .203
+   34SOL    HW2  102   -.289   -.845    .276
+   35SOL     OW  103   -.675   -.070   -.246
+   35SOL    HW1  104   -.651   -.010   -.322
+   35SOL    HW2  105   -.668   -.165   -.276
+   36SOL     OW  106    .317    .251   -.061
+   36SOL    HW1  107    .388    .322   -.055
+   36SOL    HW2  108    .229    .290   -.033
+   37SOL     OW  109   -.396   -.445   -.909
+   37SOL    HW1  110   -.455   -.439   -.829
+   37SOL    HW2  111   -.411   -.533   -.955
+   38SOL     OW  112   -.195   -.148    .572
+   38SOL    HW1  113   -.236   -.171    .484
+   38SOL    HW2  114   -.213   -.222    .637
+   39SOL     OW  115    .598    .729    .270
+   39SOL    HW1  116    .622    .798    .202
+   39SOL    HW2  117    .520    .762    .324
+   40SOL     OW  118   -.581    .345   -.918
+   40SOL    HW1  119   -.667    .295   -.931
+   40SOL    HW2  120   -.519    .291   -.862
+   41SOL     OW  121   -.286   -.200    .307
+   41SOL    HW1  122   -.197   -.154    .310
+   41SOL    HW2  123   -.307   -.224    .212
+   42SOL     OW  124    .807    .605   -.397
+   42SOL    HW1  125    .760    .602   -.308
+   42SOL    HW2  126    .756    .550   -.463
+   43SOL     OW  127   -.468    .469   -.188
+   43SOL    HW1  128   -.488    .512   -.100
+   43SOL    HW2  129   -.390    .407   -.179
+   44SOL     OW  130   -.889    .890   -.290
+   44SOL    HW1  131   -.843    .806   -.319
+   44SOL    HW2  132   -.945    .924   -.365
+   45SOL     OW  133   -.871    .410   -.620
+   45SOL    HW1  134   -.948    .444   -.566
+   45SOL    HW2  135   -.905    .359   -.699
+   46SOL     OW  136   -.821    .701    .429
+   46SOL    HW1  137   -.795    .697    .525
+   46SOL    HW2  138   -.906    .650    .415
+   47SOL     OW  139    .076    .811    .789
+   47SOL    HW1  140    .175    .799    .798
+   47SOL    HW2  141    .052    .906    .810
+   48SOL     OW  142    .130   -.041   -.291
+   48SOL    HW1  143    .120   -.056   -.192
+   48SOL    HW2  144    .044   -.005   -.327
+   49SOL     OW  145    .865    .348    .195
+   49SOL    HW1  146    .924    .411    .146
+   49SOL    HW2  147    .884    .254    .166
+   50SOL     OW  148   -.143    .585   -.031
+   50SOL    HW1  149   -.169    .674   -.067
+   50SOL    HW2  150   -.145    .517   -.104
+   51SOL     OW  151   -.500   -.718    .545
+   51SOL    HW1  152   -.417   -.747    .497
+   51SOL    HW2  153   -.549   -.651    .489
+   52SOL     OW  154    .550    .196    .885
+   52SOL    HW1  155    .545    .191    .985
+   52SOL    HW2  156    .552    .292    .856
+   53SOL     OW  157   -.854   -.406    .477
+   53SOL    HW1  158   -.900   -.334    .425
+   53SOL    HW2  159   -.858   -.386    .575
+   54SOL     OW  160    .351   -.061    .853
+   54SOL    HW1  161    .401   -.147    .859
+   54SOL    HW2  162    .416    .016    .850
+   55SOL     OW  163   -.067   -.796    .873
+   55SOL    HW1  164   -.129   -.811    .797
+   55SOL    HW2  165   -.119   -.785    .958
+   56SOL     OW  166   -.635   -.312   -.356
+   56SOL    HW1  167   -.629   -.389   -.292
+   56SOL    HW2  168   -.687   -.338   -.436
+   57SOL     OW  169    .321   -.919    .242
+   57SOL    HW1  170    .403   -.880    .200
+   57SOL    HW2  171    .294  -1.001    .193
+   58SOL     OW  172   -.404    .735    .728
+   58SOL    HW1  173   -.409    .670    .803
+   58SOL    HW2  174   -.324    .794    .741
+   59SOL     OW  175    .461   -.596   -.135
+   59SOL    HW1  176    .411   -.595   -.221
+   59SOL    HW2  177    .398   -.614   -.059
+   60SOL     OW  178   -.751   -.086    .237
+   60SOL    HW1  179   -.811   -.148    .287
+   60SOL    HW2  180   -.720   -.130    .152
+   61SOL     OW  181    .202    .285   -.364
+   61SOL    HW1  182    .122    .345   -.377
+   61SOL    HW2  183    .192    .236   -.278
+   62SOL     OW  184   -.230   -.485    .081
+   62SOL    HW1  185   -.262   -.391    .071
+   62SOL    HW2  186   -.306   -.548    .069
+   63SOL     OW  187    .464   -.119    .323
+   63SOL    HW1  188    .497   -.080    .409
+   63SOL    HW2  189    .540   -.126    .258
+   64SOL     OW  190   -.462    .107    .426
+   64SOL    HW1  191   -.486    .070    .336
+   64SOL    HW2  192   -.363    .123    .430
+   65SOL     OW  193    .249   -.077   -.621
+   65SOL    HW1  194    .306   -.142   -.571
+   65SOL    HW2  195    .233   -.110   -.714
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+  202SOL    HW1  605    .594   -.521   -.200
+  202SOL    HW2  606    .669   -.376   -.207
+  203SOL     OW  607   -.038    .192   -.635
+  203SOL    HW1  608   -.042    .102   -.591
+  203SOL    HW2  609   -.035    .181   -.734
+  204SOL     OW  610    .428    .424    .520
+  204SOL    HW1  611    .458    .352    .458
+  204SOL    HW2  612    .389    .384    .603
+  205SOL     OW  613   -.157   -.375   -.758
+  205SOL    HW1  614   -.250   -.400   -.785
+  205SOL    HW2  615   -.131   -.425   -.676
+  206SOL     OW  616    .317    .547   -.582
+  206SOL    HW1  617    .355    .488   -.510
+  206SOL    HW2  618    .357    .521   -.670
+  207SOL     OW  619    .812   -.276    .687
+  207SOL    HW1  620    .844   -.266    .593
+  207SOL    HW2  621    .733   -.338    .689
+  208SOL     OW  622   -.438    .214   -.750
+  208SOL    HW1  623   -.386    .149   -.695
+  208SOL    HW2  624   -.487    .277   -.689
+  209SOL     OW  625   -.861    .034   -.708
+  209SOL    HW1  626   -.924   -.038   -.739
+  209SOL    HW2  627   -.768   -.002   -.708
+  210SOL     OW  628    .770   -.532    .301
+  210SOL    HW1  629    .724   -.619    .318
+  210SOL    HW2  630    .861   -.535    .342
+  211SOL     OW  631    .618   -.295   -.578
+  211SOL    HW1  632    .613   -.213   -.521
+  211SOL    HW2  633    .707   -.298   -.623
+  212SOL     OW  634   -.510    .052    .168
+  212SOL    HW1  635   -.475    .011    .084
+  212SOL    HW2  636   -.600    .014    .188
+  213SOL     OW  637   -.562    .453    .691
+  213SOL    HW1  638   -.621    .533    .695
+  213SOL    HW2  639   -.547    .418    .784
+  214SOL     OW  640   -.269    .221    .882
+  214SOL    HW1  641   -.353    .220    .936
+  214SOL    HW2  642   -.267    .304    .826
+  215SOL     OW  643    .039   -.785    .300
+  215SOL    HW1  644    .138   -.796    .291
+  215SOL    HW2  645   -.001   -.871    .332
+  216SOL     OW  646    .875   -.216    .337
+  216SOL    HW1  647    .798   -.251    .283
+  216SOL    HW2  648    .843   -.145    .399
+   1.86206   1.86206   1.86206

diff --git a/src/gromacs/gmxpreprocess/tests/x.gro b/src/gromacs/gmxpreprocess/tests/x.gro
new file mode 100644 (file)
index 0000000..5c43bf5
--- /dev/null
+++ b/src/gromacs/gmxpreprocess/tests/x.gro
@@ -0,0 +1,5 @@
+test molecule for insertion
+ 2
+    1X       X1    1   1.970   1.460   1.209 -0.8587 -0.1344 -0.0643
+    1X       X2    2   1.978   1.415   1.082  0.0623 -0.1787  0.0036
+   3.01000   3.01000   3.01000