MSD tests for the -mol option.

Had to free some memory as well to make tests pass.
Added basic code for running grompp.

Renamed spc5 files in simulationdatabase that are used
in src/programs/mdrun/tests to tip3p5 since they were
in fact using tip3p and in this manner a conflict with
the gmx_msd tests is avoided.

TODO: re-use the grompp code in moduletest.cpp
from src/programs/mdrun/tests

Part of #2815

Change-Id: I5d5d33f431f1d3089ebaef54b6388348d47ce6e2

diff --git a/src/gromacs/gmxana/gmx_msd.cpp b/src/gromacs/gmxana/gmx_msd.cpp
index 0ffe400b984f6491d1ea6bfa4c037fc12b59e09b..d81ce39ef95bcba6a36efad5151982ae55c07def 100644 (file)
--- a/src/gromacs/gmxana/gmx_msd.cpp
+++ b/src/gromacs/gmxana/gmx_msd.cpp
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017,2018,2019, 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.
@@ -157,6 +157,23 @@ struct t_corr {
             }
         }
     }
+    ~t_corr()
+    {
+        sfree(ndata);
+        sfree(data);
+        for (int i = 0; i < nrestart; i++)
+        {
+            for (int j = 0; j < nmol; j++)
+            {
+                gmx_stats_free(lsq[i][j]);
+            }
+        }
+        sfree(lsq);
+        if (mass)
+        {
+            sfree(mass);
+        }
+    }
 };
 
 typedef real t_calc_func (t_corr *curr, int nx, const int index[], int nx0, rvec xc[],
@@ -1204,6 +1221,7 @@ int gmx_msd(int argc, char *argv[])
             &top, ePBC, bTen, bMW, bRmCOMM, type, dim_factor, axis, dt, beginfit, endfit,
             oenv);
 
+    done_top(&top);
     view_all(oenv, NFILE, fnm);
 
     return 0;

diff --git a/src/gromacs/gmxana/tests/gmx_msd.cpp b/src/gromacs/gmxana/tests/gmx_msd.cpp
index 43e85be8836d5ebe27fbf3a3dbca7f3617f4488e..6a21280fded1f715c0d3c8d98b358df977885fc8 100644 (file)
--- a/src/gromacs/gmxana/tests/gmx_msd.cpp
+++ b/src/gromacs/gmxana/tests/gmx_msd.cpp
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2018, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019, 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.
@@ -41,8 +41,13 @@
 
 #include "gmxpre.h"
 
+#include <cstdio>
+#include <cstdlib>
+
 #include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/gmxpreprocess/grompp.h"
 #include "gromacs/utility/futil.h"
+#include "gromacs/utility/path.h"
 #include "gromacs/utility/textreader.h"
 
 #include "testutils/cmdlinetest.h"
@@ -77,6 +82,59 @@ class MsdTest : public gmx::test::CommandLineTestBase
         }
 };
 
+class MsdMolTest : public gmx::test::CommandLineTestBase
+{
+    public:
+        MsdMolTest()
+        {
+            double    tolerance = 1e-5;
+            XvgMatch  xvg;
+            XvgMatch &toler     = xvg.tolerance(gmx::test::relativeToleranceAsFloatingPoint(1, tolerance));
+            setOutputFile("-mol", "msdmol.xvg", toler);
+        }
+
+        void runTest(const CommandLine &args, const char *ndxfile,
+                     const std::string &simulationName)
+        {
+            setInputFile("-f", simulationName + ".pdb");
+            std::string tpr = fileManager().getTemporaryFilePath(".tpr");
+            std::string mdp = fileManager().getTemporaryFilePath(".mdp");
+            FILE       *fp  = fopen(mdp.c_str(), "w");
+            fprintf(fp, "cutoff-scheme = verlet\n");
+            fprintf(fp, "rcoulomb      = 0.85\n");
+            fprintf(fp, "rvdw          = 0.85\n");
+            fprintf(fp, "rlist         = 0.85\n");
+            fclose(fp);
+
+            // Prepare a .tpr file
+            {
+                CommandLine caller;
+                auto        simDB = gmx::test::TestFileManager::getTestSimulationDatabaseDirectory();
+                auto        base  = gmx::Path::join(simDB, simulationName);
+                caller.append("grompp");
+                caller.addOption("-maxwarn", 0);
+                caller.addOption("-f", mdp.c_str());
+                std::string gro = (base + ".pdb");
+                caller.addOption("-c", gro.c_str());
+                std::string top = (base + ".top");
+                caller.addOption("-p", top.c_str());
+                std::string ndx = (base + ".ndx");
+                caller.addOption("-n", ndx.c_str());
+                caller.addOption("-o", tpr.c_str());
+                ASSERT_EQ(0, gmx_grompp(caller.argc(), caller.argv()));
+            }
+            // Run the MSD analysis
+            {
+                setInputFile("-n", ndxfile);
+                CommandLine &cmdline = commandLine();
+                cmdline.merge(args);
+                cmdline.addOption("-s", tpr.c_str());
+                ASSERT_EQ(0, gmx_msd(cmdline.argc(), cmdline.argv()));
+                checkOutputFiles();
+            }
+        }
+};
+
 /* msd_traj.xtc contains a 10 frame (1 ps per frame) simulation
  * containing 3 atoms, with different starting positions but identical
  * displacements. The displacements are calculated to yield the following
@@ -113,4 +171,32 @@ TEST_F(MsdTest, oneDimensionalDiffusion)
     };
     runTest(CommandLine(cmdline));
 }
+
+// Test the diffusion per molecule output, mass weighted
+TEST_F(MsdMolTest, diffMolMassWeighted)
+{
+    const char *const cmdline[] = {
+        "msd", "-trestart", "200"
+    };
+    runTest(CommandLine(cmdline), "spc5.ndx", "spc5");
+}
+
+// Test the diffusion per molecule output, non-mass weighted
+TEST_F(MsdMolTest, diffMolNonMassWeighted)
+{
+    const char *const cmdline[] = {
+        "msd", "-trestart", "200", "-mw", "no"
+    };
+    runTest(CommandLine(cmdline), "spc5.ndx", "spc5");
+}
+
+// Test the diffusion per molecule output, with selection
+TEST_F(MsdMolTest, diffMolSelected)
+{
+    const char *const cmdline[] = {
+        "msd", "-trestart", "200"
+    };
+    runTest(CommandLine(cmdline), "spc5_3.ndx", "spc5");
+}
+
 } //namespace

diff --git a/src/gromacs/gmxana/tests/refdata/MsdMolTest_diffMolMassWeighted.xml b/src/gromacs/gmxana/tests/refdata/MsdMolTest_diffMolMassWeighted.xml
new file mode 100644 (file)
index 0000000..dfbab14
--- /dev/null
+++ b/src/gromacs/gmxana/tests/refdata/MsdMolTest_diffMolMassWeighted.xml
@@ -0,0 +1,43 @@
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+  <OutputFiles Name="Files">
+    <File Name="-mol">
+      <XvgLegend Name="Legend">
+        <String Name="XvgLegend"><![CDATA[
+title "Diffusion Coefficients / Molecule"
+xaxis  label "Molecule"
+yaxis  label "D"
+TYPE xy
+]]></String>
+      </XvgLegend>
+      <XvgData Name="Data">
+        <Sequence Name="Row0">
+          <Int Name="Length">2</Int>
+          <Real>0</Real>
+          <Real>0.747088</Real>
+        </Sequence>
+        <Sequence Name="Row1">
+          <Int Name="Length">2</Int>
+          <Real>1</Real>
+          <Real>0.129497</Real>
+        </Sequence>
+        <Sequence Name="Row2">
+          <Int Name="Length">2</Int>
+          <Real>2</Real>
+          <Real>1.00167</Real>
+        </Sequence>
+        <Sequence Name="Row3">
+          <Int Name="Length">2</Int>
+          <Real>3</Real>
+          <Real>21.2013</Real>
+        </Sequence>
+        <Sequence Name="Row4">
+          <Int Name="Length">2</Int>
+          <Real>4</Real>
+          <Real>9.28605</Real>
+        </Sequence>
+      </XvgData>
+    </File>
+  </OutputFiles>
+</ReferenceData>

diff --git a/src/gromacs/gmxana/tests/refdata/MsdMolTest_diffMolNonMassWeighted.xml b/src/gromacs/gmxana/tests/refdata/MsdMolTest_diffMolNonMassWeighted.xml
new file mode 100644 (file)
index 0000000..dfbab14
--- /dev/null
+++ b/src/gromacs/gmxana/tests/refdata/MsdMolTest_diffMolNonMassWeighted.xml
@@ -0,0 +1,43 @@
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+  <OutputFiles Name="Files">
+    <File Name="-mol">
+      <XvgLegend Name="Legend">
+        <String Name="XvgLegend"><![CDATA[
+title "Diffusion Coefficients / Molecule"
+xaxis  label "Molecule"
+yaxis  label "D"
+TYPE xy
+]]></String>
+      </XvgLegend>
+      <XvgData Name="Data">
+        <Sequence Name="Row0">
+          <Int Name="Length">2</Int>
+          <Real>0</Real>
+          <Real>0.747088</Real>
+        </Sequence>
+        <Sequence Name="Row1">
+          <Int Name="Length">2</Int>
+          <Real>1</Real>
+          <Real>0.129497</Real>
+        </Sequence>
+        <Sequence Name="Row2">
+          <Int Name="Length">2</Int>
+          <Real>2</Real>
+          <Real>1.00167</Real>
+        </Sequence>
+        <Sequence Name="Row3">
+          <Int Name="Length">2</Int>
+          <Real>3</Real>
+          <Real>21.2013</Real>
+        </Sequence>
+        <Sequence Name="Row4">
+          <Int Name="Length">2</Int>
+          <Real>4</Real>
+          <Real>9.28605</Real>
+        </Sequence>
+      </XvgData>
+    </File>
+  </OutputFiles>
+</ReferenceData>

diff --git a/src/gromacs/gmxana/tests/refdata/MsdMolTest_diffMolSelected.xml b/src/gromacs/gmxana/tests/refdata/MsdMolTest_diffMolSelected.xml
new file mode 100644 (file)
index 0000000..d315daf
--- /dev/null
+++ b/src/gromacs/gmxana/tests/refdata/MsdMolTest_diffMolSelected.xml
@@ -0,0 +1,33 @@
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+  <OutputFiles Name="Files">
+    <File Name="-mol">
+      <XvgLegend Name="Legend">
+        <String Name="XvgLegend"><![CDATA[
+title "Diffusion Coefficients / Molecule"
+xaxis  label "Molecule"
+yaxis  label "D"
+TYPE xy
+]]></String>
+      </XvgLegend>
+      <XvgData Name="Data">
+        <Sequence Name="Row0">
+          <Int Name="Length">2</Int>
+          <Real>0</Real>
+          <Real>0.747088</Real>
+        </Sequence>
+        <Sequence Name="Row1">
+          <Int Name="Length">2</Int>
+          <Real>1</Real>
+          <Real>0.129497</Real>
+        </Sequence>
+        <Sequence Name="Row2">
+          <Int Name="Length">2</Int>
+          <Real>2</Real>
+          <Real>21.2013</Real>
+        </Sequence>
+      </XvgData>
+    </File>
+  </OutputFiles>
+</ReferenceData>

diff --git a/src/programs/mdrun/tests/minimize.cpp b/src/programs/mdrun/tests/minimize.cpp
index 1ac72c7ee8464c184f3e3df692ef6806f23adf52..c35e54891586412590cf49788dd3325b86bac268 100644 (file)
--- a/src/programs/mdrun/tests/minimize.cpp
+++ b/src/programs/mdrun/tests/minimize.cpp
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2018, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019, 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.
@@ -95,7 +95,7 @@ std::unordered_map<std::string, FloatingPointTolerance> potentialEnergyTolerance
          relativeToleranceAsPrecisionDependentUlp(-1, 10, 200)
      },
      {
-         "spc5",
+         "tip3p5",
          relativeToleranceAsPrecisionDependentUlp(-50, 150, 3800)
      },
      {
@@ -189,7 +189,7 @@ TEST_P(EnergyMinimizationTest, WithinTolerances)
 std::vector<std::string> unconstrainedSystemsToTest_g = { "argon12", "glycine_no_constraints_vacuo" };
 std::vector<std::string> minimizersToTest_g           = { "steep", "cg", "l-bfgs" };
 
-std::vector<std::string> constrainedSystemsToTest_g        = { "spc5", "glycine_vacuo", "alanine_vsite_vacuo" };
+std::vector<std::string> constrainedSystemsToTest_g        = { "tip3p5", "glycine_vacuo", "alanine_vsite_vacuo" };
 std::vector<std::string> minimizersToTestWithConstraints_g = { "steep", "cg" };
 //! \}
 

diff --git a/src/programs/mdrun/tests/refdata/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0.xml b/src/programs/mdrun/tests/refdata/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0.xml
index 6899c4fb173218d21ca15ba95e708c742fe6709b..5a8f1ba94c8cbea20c058927c37b896d49628c9d 100644 (file)
--- a/src/programs/mdrun/tests/refdata/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0.xml
+++ b/src/programs/mdrun/tests/refdata/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0.xml
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
 <?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
 <ReferenceData>
-  <Simulation Name="spc5">
+  <Simulation Name="tip3p5">
     <Minimizer Name="steep">
       <Energy Name="Potential">
         <Real Name="Time 0.000000 Step 0 in frame 0">-9.6231425679441998</Real>

diff --git a/src/programs/mdrun/tests/refdata/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1.xml b/src/programs/mdrun/tests/refdata/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1.xml
index 8e75a6a95365f06ed6273012d451f37a7ad5c3d6..8f66944976d29968bd1457b62808c4e40fb3e653 100644 (file)
--- a/src/programs/mdrun/tests/refdata/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1.xml
+++ b/src/programs/mdrun/tests/refdata/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1.xml
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
 <?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
 <ReferenceData>
-  <Simulation Name="spc5">
+  <Simulation Name="tip3p5">
     <Minimizer Name="cg">
       <Energy Name="Potential">
         <Real Name="Time 0.000000 Step 0 in frame 0">-9.6231425679441998</Real>

diff --git a/src/programs/mdrun/tests/rerun.cpp b/src/programs/mdrun/tests/rerun.cpp
index d384a151a64a46656d9672ed82e014a972b56832..29d9a49c013e39a6bfeb0bfcee8abe1dbae09ef8 100644 (file)
--- a/src/programs/mdrun/tests/rerun.cpp
+++ b/src/programs/mdrun/tests/rerun.cpp
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017,2018,2019, 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.
@@ -262,11 +262,11 @@ TEST_P(MdrunRerunTest, WithinTolerances)
 // tests can run in such configurations.
 #if GMX_GPU != GMX_GPU_OPENCL
 INSTANTIATE_TEST_CASE_P(NormalMdrunIsReproduced, MdrunRerunTest,
-                            ::testing::Combine(::testing::Values("argon12", "spc5", "alanine_vsite_vacuo"),
+                            ::testing::Combine(::testing::Values("argon12", "tip3p5", "alanine_vsite_vacuo"),
                                                    ::testing::Values("md", "md-vv", "bd", "sd")));
 #else
 INSTANTIATE_TEST_CASE_P(DISABLED_NormalMdrunIsReproduced, MdrunRerunTest,
-                            ::testing::Combine(::testing::Values("argon12", "spc5", "alanine_vsite_vacuo"),
+                            ::testing::Combine(::testing::Values("argon12", "tip3p5", "alanine_vsite_vacuo"),
                                                    ::testing::Values("md", "md-vv", "bd", "sd")));
 #endif
 

diff --git a/src/testutils/simulationdatabase.cpp b/src/testutils/simulationdatabase.cpp
index 78ad2f8e5d673501d01c9f800308c19c8fbd5f81..62cafa139a41d094f056dd4ea39eb6a183911427 100644 (file)
--- a/src/testutils/simulationdatabase.cpp
+++ b/src/testutils/simulationdatabase.cpp
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2016,2018, by the GROMACS development team, led by
+ * Copyright (c) 2016,2018,2019, 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.
@@ -88,15 +88,15 @@ const MdpFileValues mdpFileValueDatabase_g
     },
     // Simple system with 5 water molecules, fairly widely separated
     {
-        "spc5", { { {
-                        "compressibility", "5e-10"
-                    },
+        "tip3p5", { { {
+                          "compressibility", "5e-10"
+                      },
+                      {
+                          "tau-p", "1000"
+                      } },
                     {
-                        "tau-p", "1000"
-                    } },
-                  {
-                      1, 2, 3, 4, 5, 6, 8, 9
-                  } }
+                        1, 2, 3, 4, 5, 6, 8, 9
+                    } }
     },
     // Simple system with 5832 argon atoms, suitable for normal pressure coupling
     {

diff --git a/src/testutils/simulationdatabase.h b/src/testutils/simulationdatabase.h
index 8298093269ba44ce850229354c2267bf01aecc1e..ae61dbc9407916dd52d18e957da707d7b488d2be 100644 (file)
--- a/src/testutils/simulationdatabase.h
+++ b/src/testutils/simulationdatabase.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2018, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019, 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.
@@ -76,7 +76,7 @@ using MdpFieldValues = std::map<std::string, std::string>;
  * comparisons is available, whose \c simulationName keys are
  *     - argon12
  *     - argon5832
- *     - spc5
+ *     - tip3p5
  *     - spc216
  *     - alanine_vsite_vacuo
  *     - alanine_vsite_solvated

diff --git a/src/testutils/simulationdatabase/spc5.ndx b/src/testutils/simulationdatabase/spc5.ndx
index c678461c5c0b6d875a7a59dbf4efaf254d3347a6..f4d5754aee8c877064203085958d8e6fe22ad769 100644 (file)
--- a/src/testutils/simulationdatabase/spc5.ndx
+++ b/src/testutils/simulationdatabase/spc5.ndx
@@ -1,2 +1,3 @@
-[ System ]
-   1    2    3    4    5    6    7    8    9   10   11   12   13   14   15 
+[ water ]
+1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
+

diff --git a/src/testutils/simulationdatabase/spc5.pdb b/src/testutils/simulationdatabase/spc5.pdb
new file mode 100644 (file)
index 0000000..bdfa478
--- /dev/null
+++ b/src/testutils/simulationdatabase/spc5.pdb
@@ -0,0 +1,572 @@
+REMARK    GENERATED BY TRJCONV
+TITLE     water t=   0.00000 step= 0
+REMARK    THIS IS A SIMULATION BOX
+CRYST1   18.621   18.621   18.621  90.00  90.00  90.00 P 1           1
+MODEL        1
+ATOM      1  OW  SOL     1      15.330   9.890   2.320  1.00  0.00           O
+ATOM      2  HW1 SOL     1      14.660   9.590   1.570  1.00  0.00           H
+ATOM      3  HW2 SOL     1      16.140  10.370   1.940  1.00  0.00           H
+ATOM      4  OW  SOL     2       2.280   7.430  11.030  1.00  0.00           O
+ATOM      5  HW1 SOL     2       1.510   8.060  11.060  1.00  0.00           H
+ATOM      6  HW2 SOL     2       2.870   7.560  11.840  1.00  0.00           H
+ATOM      7  OW  SOL     3      12.700   6.440   2.270  1.00  0.00           O
+ATOM      8  HW1 SOL     3      12.510   7.190   1.580  1.00  0.00           H
+ATOM      9  HW2 SOL     3      13.090   5.670   1.730  1.00  0.00           H
+ATOM     10  OW  SOL     4       4.350  18.020   9.590  1.00  0.00           O
+ATOM     11  HW1 SOL     4       4.350  18.060  10.600  1.00  0.00           H
+ATOM     12  HW2 SOL     4       3.370  18.160   9.350  1.00  0.00           H
+ATOM     13  OW  SOL     5       3.080  11.360   9.950  1.00  0.00           O
+ATOM     14  HW1 SOL     5       2.890  12.320  10.040  1.00  0.00           H
+ATOM     15  HW2 SOL     5       3.360  11.090  10.880  1.00  0.00           H
+TER
+ENDMDL
+REMARK    GENERATED BY TRJCONV
+TITLE     water t=   0.00400 step= 20
+REMARK    THIS IS A SIMULATION BOX
+CRYST1   18.621   18.621   18.621  90.00  90.00  90.00 P 1           1
+MODEL        2
+ATOM      1  OW  SOL     1      15.360   9.890   2.320  1.00  0.00           O
+ATOM      2  HW1 SOL     1      14.740   9.620   1.560  1.00  0.00           H
+ATOM      3  HW2 SOL     1      16.160  10.400   1.920  1.00  0.00           H
+ATOM      4  OW  SOL     2       2.280   7.430  11.000  1.00  0.00           O
+ATOM      5  HW1 SOL     2       1.530   8.190  11.010  1.00  0.00           H
+ATOM      6  HW2 SOL     2       2.860   7.650  11.850  1.00  0.00           H
+ATOM      7  OW  SOL     3      12.670   6.450   2.280  1.00  0.00           O
+ATOM      8  HW1 SOL     3      12.500   7.180   1.640  1.00  0.00           H
+ATOM      9  HW2 SOL     3      13.140   5.720   1.750  1.00  0.00           H
+ATOM     10  OW  SOL     4       4.330  18.040   9.590  1.00  0.00           O
+ATOM     11  HW1 SOL     4       4.280  18.100  10.610  1.00  0.00           H
+ATOM     12  HW2 SOL     4       3.360  18.140   9.330  1.00  0.00           H
+ATOM     13  OW  SOL     5       3.080  11.340   9.940  1.00  0.00           O
+ATOM     14  HW1 SOL     5       2.820  12.330  10.000  1.00  0.00           H
+ATOM     15  HW2 SOL     5       3.280  11.140  10.900  1.00  0.00           H
+TER
+ENDMDL
+REMARK    GENERATED BY TRJCONV
+TITLE     water t=   0.00800 step= 40
+REMARK    THIS IS A SIMULATION BOX
+CRYST1   18.621   18.621   18.621  90.00  90.00  90.00 P 1           1
+MODEL        3
+ATOM      1  OW  SOL     1      15.400   9.890   2.330  1.00  0.00           O
+ATOM      2  HW1 SOL     1      14.800   9.670   1.540  1.00  0.00           H
+ATOM      3  HW2 SOL     1      16.130  10.390   1.880  1.00  0.00           H
+ATOM      4  OW  SOL     2       2.280   7.430  10.970  1.00  0.00           O
+ATOM      5  HW1 SOL     2       1.670   8.180  10.950  1.00  0.00           H
+ATOM      6  HW2 SOL     2       2.800   7.680  11.790  1.00  0.00           H
+ATOM      7  OW  SOL     3      12.650   6.450   2.290  1.00  0.00           O
+ATOM      8  HW1 SOL     3      12.520   7.210   1.650  1.00  0.00           H
+ATOM      9  HW2 SOL     3      13.190   5.770   1.750  1.00  0.00           H
+ATOM     10  OW  SOL     4       4.310  18.050   9.590  1.00  0.00           O
+ATOM     11  HW1 SOL     4       4.220  18.120  10.590  1.00  0.00           H
+ATOM     12  HW2 SOL     4       3.330  18.130   9.280  1.00  0.00           H
+ATOM     13  OW  SOL     5       3.080  11.330   9.930  1.00  0.00           O
+ATOM     14  HW1 SOL     5       2.770  12.310   9.910  1.00  0.00           H
+ATOM     15  HW2 SOL     5       3.210  11.140  10.970  1.00  0.00           H
+TER
+ENDMDL
+REMARK    GENERATED BY TRJCONV
+TITLE     water t=   0.01200 step= 60
+REMARK    THIS IS A SIMULATION BOX
+CRYST1   18.621   18.621   18.621  90.00  90.00  90.00 P 1           1
+MODEL        4
+ATOM      1  OW  SOL     1      15.430   9.890   2.350  1.00  0.00           O
+ATOM      2  HW1 SOL     1      14.800   9.690   1.530  1.00  0.00           H
+ATOM      3  HW2 SOL     1      16.160  10.410   1.830  1.00  0.00           H
+ATOM      4  OW  SOL     2       2.290   7.440  10.950  1.00  0.00           O
+ATOM      5  HW1 SOL     2       1.660   8.260  10.840  1.00  0.00           H
+ATOM      6  HW2 SOL     2       2.810   7.660  11.810  1.00  0.00           H
+ATOM      7  OW  SOL     3      12.620   6.450   2.290  1.00  0.00           O
+ATOM      8  HW1 SOL     3      12.530   7.250   1.650  1.00  0.00           H
+ATOM      9  HW2 SOL     3      13.230   5.840   1.750  1.00  0.00           H
+ATOM     10  OW  SOL     4       4.290  18.070   9.590  1.00  0.00           O
+ATOM     11  HW1 SOL     4       4.170  18.160  10.600  1.00  0.00           H
+ATOM     12  HW2 SOL     4       3.350  18.150   9.230  1.00  0.00           H
+ATOM     13  OW  SOL     5       3.070  11.320   9.930  1.00  0.00           O
+ATOM     14  HW1 SOL     5       2.760  12.250   9.790  1.00  0.00           H
+ATOM     15  HW2 SOL     5       3.120  11.170  10.900  1.00  0.00           H
+TER
+ENDMDL
+REMARK    GENERATED BY TRJCONV
+TITLE     water t=   0.01600 step= 80
+REMARK    THIS IS A SIMULATION BOX
+CRYST1   18.621   18.621   18.621  90.00  90.00  90.00 P 1           1
+MODEL        5
+ATOM      1  OW  SOL     1      15.460   9.890   2.350  1.00  0.00           O
+ATOM      2  HW1 SOL     1      14.790   9.690   1.640  1.00  0.00           H
+ATOM      3  HW2 SOL     1      16.180  10.400   1.840  1.00  0.00           H
+ATOM      4  OW  SOL     2       2.290   7.450  10.930  1.00  0.00           O
+ATOM      5  HW1 SOL     2       1.670   8.260  10.730  1.00  0.00           H
+ATOM      6  HW2 SOL     2       2.820   7.600  11.810  1.00  0.00           H
+ATOM      7  OW  SOL     3      12.600   6.450   2.290  1.00  0.00           O
+ATOM      8  HW1 SOL     3      12.540   7.240   1.730  1.00  0.00           H
+ATOM      9  HW2 SOL     3      13.260   5.880   1.760  1.00  0.00           H
+ATOM     10  OW  SOL     4       4.260  18.090   9.590  1.00  0.00           O
+ATOM     11  HW1 SOL     4       4.110  18.190  10.590  1.00  0.00           H
+ATOM     12  HW2 SOL     4       3.340  18.200   9.170  1.00  0.00           H
+ATOM     13  OW  SOL     5       3.060  11.310   9.920  1.00  0.00           O
+ATOM     14  HW1 SOL     5       2.740  12.260   9.670  1.00  0.00           H
+ATOM     15  HW2 SOL     5       3.060  11.200  10.950  1.00  0.00           H
+TER
+ENDMDL
+REMARK    GENERATED BY TRJCONV
+TITLE     water t=   0.02000 step= 100
+REMARK    THIS IS A SIMULATION BOX
+CRYST1   18.621   18.621   18.621  90.00  90.00  90.00 P 1           1
+MODEL        6
+ATOM      1  OW  SOL     1      15.500   9.880   2.360  1.00  0.00           O
+ATOM      2  HW1 SOL     1      14.720   9.690   1.710  1.00  0.00           H
+ATOM      3  HW2 SOL     1      16.210  10.380   1.840  1.00  0.00           H
+ATOM      4  OW  SOL     2       2.290   7.460  10.910  1.00  0.00           O
+ATOM      5  HW1 SOL     2       1.740   8.210  10.680  1.00  0.00           H
+ATOM      6  HW2 SOL     2       2.760   7.580  11.780  1.00  0.00           H
+ATOM      7  OW  SOL     3      12.590   6.450   2.290  1.00  0.00           O
+ATOM      8  HW1 SOL     3      12.510   7.330   1.770  1.00  0.00           H
+ATOM      9  HW2 SOL     3      13.260   5.880   1.780  1.00  0.00           H
+ATOM     10  OW  SOL     4       4.230  18.100   9.590  1.00  0.00           O
+ATOM     11  HW1 SOL     4       4.040  18.240  10.580  1.00  0.00           H
+ATOM     12  HW2 SOL     4       3.340  18.280   9.130  1.00  0.00           H
+ATOM     13  OW  SOL     5       3.050  11.290   9.900  1.00  0.00           O
+ATOM     14  HW1 SOL     5       2.750  12.200   9.610  1.00  0.00           H
+ATOM     15  HW2 SOL     5       3.020  11.270  10.950  1.00  0.00           H
+TER
+ENDMDL
+REMARK    GENERATED BY TRJCONV
+TITLE     water t=   0.02400 step= 120
+REMARK    THIS IS A SIMULATION BOX
+CRYST1   18.621   18.621   18.621  90.00  90.00  90.00 P 1           1
+MODEL        7
+ATOM      1  OW  SOL     1      15.520   9.880   2.380  1.00  0.00           O
+ATOM      2  HW1 SOL     1      14.710   9.720   1.780  1.00  0.00           H
+ATOM      3  HW2 SOL     1      16.250  10.350   1.790  1.00  0.00           H
+ATOM      4  OW  SOL     2       2.300   7.460  10.880  1.00  0.00           O
+ATOM      5  HW1 SOL     2       1.710   8.320  10.660  1.00  0.00           H
+ATOM      6  HW2 SOL     2       2.720   7.630  11.830  1.00  0.00           H
+ATOM      7  OW  SOL     3      12.580   6.450   2.280  1.00  0.00           O
+ATOM      8  HW1 SOL     3      12.480   7.350   1.850  1.00  0.00           H
+ATOM      9  HW2 SOL     3      13.260   5.880   1.800  1.00  0.00           H
+ATOM     10  OW  SOL     4       4.200  18.110   9.590  1.00  0.00           O
+ATOM     11  HW1 SOL     4       3.960  18.290  10.570  1.00  0.00           H
+ATOM     12  HW2 SOL     4       3.350  18.380   9.120  1.00  0.00           H
+ATOM     13  OW  SOL     5       3.040  11.280   9.890  1.00  0.00           O
+ATOM     14  HW1 SOL     5       2.760  12.170   9.550  1.00  0.00           H
+ATOM     15  HW2 SOL     5       3.000  11.340  10.870  1.00  0.00           H
+TER
+ENDMDL
+REMARK    GENERATED BY TRJCONV
+TITLE     water t=   0.02800 step= 140
+REMARK    THIS IS A SIMULATION BOX
+CRYST1   18.621   18.621   18.621  90.00  90.00  90.00 P 1           1
+MODEL        8
+ATOM      1  OW  SOL     1      15.550   9.870   2.390  1.00  0.00           O
+ATOM      2  HW1 SOL     1      14.740   9.770   1.820  1.00  0.00           H
+ATOM      3  HW2 SOL     1      16.220  10.270   1.740  1.00  0.00           H
+ATOM      4  OW  SOL     2       2.310   7.460  10.860  1.00  0.00           O
+ATOM      5  HW1 SOL     2       1.770   8.270  10.690  1.00  0.00           H
+ATOM      6  HW2 SOL     2       2.650   7.670  11.810  1.00  0.00           H
+ATOM      7  OW  SOL     3      12.570   6.450   2.280  1.00  0.00           O
+ATOM      8  HW1 SOL     3      12.460   7.360   1.900  1.00  0.00           H
+ATOM      9  HW2 SOL     3      13.250   5.900   1.760  1.00  0.00           H
+ATOM     10  OW  SOL     4       4.170  18.130   9.590  1.00  0.00           O
+ATOM     11  HW1 SOL     4       3.900  18.320  10.550  1.00  0.00           H
+ATOM     12  HW2 SOL     4       3.360  18.490   9.080  1.00  0.00           H
+ATOM     13  OW  SOL     5       3.030  11.260   9.870  1.00  0.00           O
+ATOM     14  HW1 SOL     5       2.750  12.170   9.480  1.00  0.00           H
+ATOM     15  HW2 SOL     5       3.000  11.380  10.930  1.00  0.00           H
+TER
+ENDMDL
+REMARK    GENERATED BY TRJCONV
+TITLE     water t=   0.03200 step= 160
+REMARK    THIS IS A SIMULATION BOX
+CRYST1   18.621   18.621   18.621  90.00  90.00  90.00 P 1           1
+MODEL        9
+ATOM      1  OW  SOL     1      15.580   9.870   2.410  1.00  0.00           O
+ATOM      2  HW1 SOL     1      14.710   9.800   1.840  1.00  0.00           H
+ATOM      3  HW2 SOL     1      16.240  10.190   1.690  1.00  0.00           H
+ATOM      4  OW  SOL     2       2.320   7.470  10.850  1.00  0.00           O
+ATOM      5  HW1 SOL     2       1.750   8.270  10.670  1.00  0.00           H
+ATOM      6  HW2 SOL     2       2.620   7.650  11.790  1.00  0.00           H
+ATOM      7  OW  SOL     3      12.560   6.440   2.280  1.00  0.00           O
+ATOM      8  HW1 SOL     3      12.430   7.410   1.890  1.00  0.00           H
+ATOM      9  HW2 SOL     3      13.220   5.970   1.670  1.00  0.00           H
+ATOM     10  OW  SOL     4       4.140  18.140   9.590  1.00  0.00           O
+ATOM     11  HW1 SOL     4       3.860  18.340  10.560  1.00  0.00           H
+ATOM     12  HW2 SOL     4       3.410  18.590   9.050  1.00  0.00           H
+ATOM     13  OW  SOL     5       3.020  11.250   9.850  1.00  0.00           O
+ATOM     14  HW1 SOL     5       2.760  12.100   9.430  1.00  0.00           H
+ATOM     15  HW2 SOL     5       3.000  11.340  10.850  1.00  0.00           H
+TER
+ENDMDL
+REMARK    GENERATED BY TRJCONV
+TITLE     water t=   0.03600 step= 180
+REMARK    THIS IS A SIMULATION BOX
+CRYST1   18.621   18.621   18.621  90.00  90.00  90.00 P 1           1
+MODEL       10
+ATOM      1  OW  SOL     1      15.600   9.860   2.420  1.00  0.00           O
+ATOM      2  HW1 SOL     1      14.720   9.830   1.920  1.00  0.00           H
+ATOM      3  HW2 SOL     1      16.300  10.110   1.700  1.00  0.00           H
+ATOM      4  OW  SOL     2       2.320   7.470  10.830  1.00  0.00           O
+ATOM      5  HW1 SOL     2       1.690   8.290  10.610  1.00  0.00           H
+ATOM      6  HW2 SOL     2       2.670   7.590  11.830  1.00  0.00           H
+ATOM      7  OW  SOL     3      12.550   6.440   2.270  1.00  0.00           O
+ATOM      8  HW1 SOL     3      12.380   7.350   1.930  1.00  0.00           H
+ATOM      9  HW2 SOL     3      13.170   6.050   1.550  1.00  0.00           H
+ATOM     10  OW  SOL     4       4.100  18.160   9.590  1.00  0.00           O
+ATOM     11  HW1 SOL     4       3.840  18.330  10.570  1.00  0.00           H
+ATOM     12  HW2 SOL     4       3.450  18.680   9.020  1.00  0.00           H
+ATOM     13  OW  SOL     5       3.010  11.230   9.830  1.00  0.00           O
+ATOM     14  HW1 SOL     5       2.740  12.100   9.370  1.00  0.00           H
+ATOM     15  HW2 SOL     5       2.970  11.290  10.840  1.00  0.00           H
+TER
+ENDMDL
+REMARK    GENERATED BY TRJCONV
+TITLE     water t=   0.04000 step= 200
+REMARK    THIS IS A SIMULATION BOX
+CRYST1   18.621   18.621   18.621  90.00  90.00  90.00 P 1           1
+MODEL       11
+ATOM      1  OW  SOL     1      15.610   9.850   2.430  1.00  0.00           O
+ATOM      2  HW1 SOL     1      14.700   9.840   1.980  1.00  0.00           H
+ATOM      3  HW2 SOL     1      16.340  10.050   1.750  1.00  0.00           H
+ATOM      4  OW  SOL     2       2.320   7.470  10.820  1.00  0.00           O
+ATOM      5  HW1 SOL     2       1.730   8.200  10.620  1.00  0.00           H
+ATOM      6  HW2 SOL     2       2.690   7.530  11.770  1.00  0.00           H
+ATOM      7  OW  SOL     3      12.560   6.430   2.260  1.00  0.00           O
+ATOM      8  HW1 SOL     3      12.260   7.380   1.970  1.00  0.00           H
+ATOM      9  HW2 SOL     3      13.090   6.110   1.470  1.00  0.00           H
+ATOM     10  OW  SOL     4       4.070  18.180   9.600  1.00  0.00           O
+ATOM     11  HW1 SOL     4       3.790  18.310  10.570  1.00  0.00           H
+ATOM     12  HW2 SOL     4       3.460  18.760   9.010  1.00  0.00           H
+ATOM     13  OW  SOL     5       3.000  11.220   9.800  1.00  0.00           O
+ATOM     14  HW1 SOL     5       2.700  12.090   9.380  1.00  0.00           H
+ATOM     15  HW2 SOL     5       2.910  11.260  10.870  1.00  0.00           H
+TER
+ENDMDL
+REMARK    GENERATED BY TRJCONV
+TITLE     water t=   0.04400 step= 220
+REMARK    THIS IS A SIMULATION BOX
+CRYST1   18.621   18.621   18.621  90.00  90.00  90.00 P 1           1
+MODEL       12
+ATOM      1  OW  SOL     1      15.630   9.850   2.450  1.00  0.00           O
+ATOM      2  HW1 SOL     1      14.710   9.860   1.970  1.00  0.00           H
+ATOM      3  HW2 SOL     1      16.390  10.020   1.750  1.00  0.00           H
+ATOM      4  OW  SOL     2       2.330   7.470  10.810  1.00  0.00           O
+ATOM      5  HW1 SOL     2       1.680   8.270  10.670  1.00  0.00           H
+ATOM      6  HW2 SOL     2       2.710   7.520  11.750  1.00  0.00           H
+ATOM      7  OW  SOL     3      12.560   6.430   2.250  1.00  0.00           O
+ATOM      8  HW1 SOL     3      12.130   7.350   2.040  1.00  0.00           H
+ATOM      9  HW2 SOL     3      13.020   6.140   1.390  1.00  0.00           H
+ATOM     10  OW  SOL     4       4.040  18.200   9.600  1.00  0.00           O
+ATOM     11  HW1 SOL     4       3.720  18.300  10.570  1.00  0.00           H
+ATOM     12  HW2 SOL     4       3.460  18.820   9.060  1.00  0.00           H
+ATOM     13  OW  SOL     5       2.990  11.210   9.780  1.00  0.00           O
+ATOM     14  HW1 SOL     5       2.660  12.080   9.430  1.00  0.00           H
+ATOM     15  HW2 SOL     5       2.830  11.220  10.750  1.00  0.00           H
+TER
+ENDMDL
+REMARK    GENERATED BY TRJCONV
+TITLE     water t=   0.04800 step= 240
+REMARK    THIS IS A SIMULATION BOX
+CRYST1   18.621   18.621   18.621  90.00  90.00  90.00 P 1           1
+MODEL       13
+ATOM      1  OW  SOL     1      15.630   9.840   2.470  1.00  0.00           O
+ATOM      2  HW1 SOL     1      14.790   9.880   1.930  1.00  0.00           H
+ATOM      3  HW2 SOL     1      16.360  10.010   1.770  1.00  0.00           H
+ATOM      4  OW  SOL     2       2.330   7.460  10.790  1.00  0.00           O
+ATOM      5  HW1 SOL     2       1.700   8.270  10.770  1.00  0.00           H
+ATOM      6  HW2 SOL     2       2.720   7.540  11.770  1.00  0.00           H
+ATOM      7  OW  SOL     3      12.560   6.440   2.240  1.00  0.00           O
+ATOM      8  HW1 SOL     3      12.040   7.270   2.140  1.00  0.00           H
+ATOM      9  HW2 SOL     3      12.960   6.170   1.340  1.00  0.00           H
+ATOM     10  OW  SOL     4       4.010  18.220   9.600  1.00  0.00           O
+ATOM     11  HW1 SOL     4       3.660  18.270  10.550  1.00  0.00           H
+ATOM     12  HW2 SOL     4       3.410  18.880   9.100  1.00  0.00           H
+ATOM     13  OW  SOL     5       2.980  11.210   9.760  1.00  0.00           O
+ATOM     14  HW1 SOL     5       2.600  12.110   9.460  1.00  0.00           H
+ATOM     15  HW2 SOL     5       2.740  11.150  10.780  1.00  0.00           H
+TER
+ENDMDL
+REMARK    GENERATED BY TRJCONV
+TITLE     water t=   0.05200 step= 260
+REMARK    THIS IS A SIMULATION BOX
+CRYST1   18.621   18.621   18.621  90.00  90.00  90.00 P 1           1
+MODEL       14
+ATOM      1  OW  SOL     1      15.640   9.830   2.490  1.00  0.00           O
+ATOM      2  HW1 SOL     1      14.820   9.880   1.850  1.00  0.00           H
+ATOM      3  HW2 SOL     1      16.360  10.030   1.800  1.00  0.00           H
+ATOM      4  OW  SOL     2       2.330   7.460  10.780  1.00  0.00           O
+ATOM      5  HW1 SOL     2       1.730   8.230  10.850  1.00  0.00           H
+ATOM      6  HW2 SOL     2       2.720   7.520  11.690  1.00  0.00           H
+ATOM      7  OW  SOL     3      12.570   6.430   2.220  1.00  0.00           O
+ATOM      8  HW1 SOL     3      11.940   7.270   2.180  1.00  0.00           H
+ATOM      9  HW2 SOL     3      12.890   6.240   1.290  1.00  0.00           H
+ATOM     10  OW  SOL     4       3.980  18.240   9.600  1.00  0.00           O
+ATOM     11  HW1 SOL     4       3.620  18.200  10.560  1.00  0.00           H
+ATOM     12  HW2 SOL     4       3.360  18.890   9.130  1.00  0.00           H
+ATOM     13  OW  SOL     5       2.960  11.210   9.740  1.00  0.00           O
+ATOM     14  HW1 SOL     5       2.570  12.090   9.480  1.00  0.00           H
+ATOM     15  HW2 SOL     5       2.710  11.050  10.740  1.00  0.00           H
+TER
+ENDMDL
+REMARK    GENERATED BY TRJCONV
+TITLE     water t=   0.05600 step= 280
+REMARK    THIS IS A SIMULATION BOX
+CRYST1   18.621   18.621   18.621  90.00  90.00  90.00 P 1           1
+MODEL       15
+ATOM      1  OW  SOL     1      15.630   9.830   2.500  1.00  0.00           O
+ATOM      2  HW1 SOL     1      14.850   9.850   1.850  1.00  0.00           H
+ATOM      3  HW2 SOL     1      16.420  10.070   1.850  1.00  0.00           H
+ATOM      4  OW  SOL     2       2.330   7.460  10.770  1.00  0.00           O
+ATOM      5  HW1 SOL     2       1.660   8.280  10.860  1.00  0.00           H
+ATOM      6  HW2 SOL     2       2.790   7.440  11.700  1.00  0.00           H
+ATOM      7  OW  SOL     3      12.570   6.430   2.210  1.00  0.00           O
+ATOM      8  HW1 SOL     3      11.950   7.210   2.190  1.00  0.00           H
+ATOM      9  HW2 SOL     3      12.840   6.320   1.220  1.00  0.00           H
+ATOM     10  OW  SOL     4       3.960  18.270   9.590  1.00  0.00           O
+ATOM     11  HW1 SOL     4       3.630  18.110  10.550  1.00  0.00           H
+ATOM     12  HW2 SOL     4       3.290  18.870   9.130  1.00  0.00           H
+ATOM     13  OW  SOL     5       2.940  11.220   9.730  1.00  0.00           O
+ATOM     14  HW1 SOL     5       2.540  12.100   9.490  1.00  0.00           H
+ATOM     15  HW2 SOL     5       2.720  10.970  10.660  1.00  0.00           H
+TER
+ENDMDL
+REMARK    GENERATED BY TRJCONV
+TITLE     water t=   0.06000 step= 300
+REMARK    THIS IS A SIMULATION BOX
+CRYST1   18.621   18.621   18.621  90.00  90.00  90.00 P 1           1
+MODEL       16
+ATOM      1  OW  SOL     1      15.620   9.840   2.510  1.00  0.00           O
+ATOM      2  HW1 SOL     1      14.850   9.800   1.850  1.00  0.00           H
+ATOM      3  HW2 SOL     1      16.440  10.110   1.970  1.00  0.00           H
+ATOM      4  OW  SOL     2       2.320   7.460  10.770  1.00  0.00           O
+ATOM      5  HW1 SOL     2       1.680   8.210  10.830  1.00  0.00           H
+ATOM      6  HW2 SOL     2       2.840   7.380  11.660  1.00  0.00           H
+ATOM      7  OW  SOL     3      12.570   6.420   2.200  1.00  0.00           O
+ATOM      8  HW1 SOL     3      11.960   7.220   2.210  1.00  0.00           H
+ATOM      9  HW2 SOL     3      12.800   6.370   1.230  1.00  0.00           H
+ATOM     10  OW  SOL     4       3.940  18.290   9.590  1.00  0.00           O
+ATOM     11  HW1 SOL     4       3.640  18.030  10.520  1.00  0.00           H
+ATOM     12  HW2 SOL     4       3.180  18.830   9.130  1.00  0.00           H
+ATOM     13  OW  SOL     5       2.920  11.220   9.710  1.00  0.00           O
+ATOM     14  HW1 SOL     5       2.500  12.140   9.530  1.00  0.00           H
+ATOM     15  HW2 SOL     5       2.700  10.920  10.710  1.00  0.00           H
+TER
+ENDMDL
+REMARK    GENERATED BY TRJCONV
+TITLE     water t=   0.06400 step= 320
+REMARK    THIS IS A SIMULATION BOX
+CRYST1   18.621   18.621   18.621  90.00  90.00  90.00 P 1           1
+MODEL       17
+ATOM      1  OW  SOL     1      15.610   9.840   2.520  1.00  0.00           O
+ATOM      2  HW1 SOL     1      14.850   9.760   1.820  1.00  0.00           H
+ATOM      3  HW2 SOL     1      16.460  10.180   2.030  1.00  0.00           H
+ATOM      4  OW  SOL     2       2.320   7.460  10.760  1.00  0.00           O
+ATOM      5  HW1 SOL     2       1.640   8.220  10.830  1.00  0.00           H
+ATOM      6  HW2 SOL     2       2.820   7.400  11.610  1.00  0.00           H
+ATOM      7  OW  SOL     3      12.570   6.410   2.190  1.00  0.00           O
+ATOM      8  HW1 SOL     3      11.950   7.250   2.270  1.00  0.00           H
+ATOM      9  HW2 SOL     3      12.800   6.370   1.210  1.00  0.00           H
+ATOM     10  OW  SOL     4       3.920  18.310   9.580  1.00  0.00           O
+ATOM     11  HW1 SOL     4       3.620  17.970  10.500  1.00  0.00           H
+ATOM     12  HW2 SOL     4       3.090  18.740   9.170  1.00  0.00           H
+ATOM     13  OW  SOL     5       2.890  11.230   9.700  1.00  0.00           O
+ATOM     14  HW1 SOL     5       2.490  12.130   9.620  1.00  0.00           H
+ATOM     15  HW2 SOL     5       2.720  10.970  10.650  1.00  0.00           H
+TER
+ENDMDL
+REMARK    GENERATED BY TRJCONV
+TITLE     water t=   0.06800 step= 340
+REMARK    THIS IS A SIMULATION BOX
+CRYST1   18.621   18.621   18.621  90.00  90.00  90.00 P 1           1
+MODEL       18
+ATOM      1  OW  SOL     1      15.590   9.840   2.530  1.00  0.00           O
+ATOM      2  HW1 SOL     1      14.920   9.730   1.790  1.00  0.00           H
+ATOM      3  HW2 SOL     1      16.410  10.250   2.030  1.00  0.00           H
+ATOM      4  OW  SOL     2       2.320   7.460  10.750  1.00  0.00           O
+ATOM      5  HW1 SOL     2       1.620   8.250  10.860  1.00  0.00           H
+ATOM      6  HW2 SOL     2       2.830   7.490  11.680  1.00  0.00           H
+ATOM      7  OW  SOL     3      12.570   6.420   2.180  1.00  0.00           O
+ATOM      8  HW1 SOL     3      12.010   7.220   2.330  1.00  0.00           H
+ATOM      9  HW2 SOL     3      12.810   6.320   1.200  1.00  0.00           H
+ATOM     10  OW  SOL     4       3.900  18.320   9.570  1.00  0.00           O
+ATOM     11  HW1 SOL     4       3.600  17.950  10.460  1.00  0.00           H
+ATOM     12  HW2 SOL     4       2.990  18.660   9.190  1.00  0.00           H
+ATOM     13  OW  SOL     5       2.860  11.240   9.680  1.00  0.00           O
+ATOM     14  HW1 SOL     5       2.480  12.170   9.680  1.00  0.00           H
+ATOM     15  HW2 SOL     5       2.750  11.010  10.670  1.00  0.00           H
+TER
+ENDMDL
+REMARK    GENERATED BY TRJCONV
+TITLE     water t=   0.07200 step= 360
+REMARK    THIS IS A SIMULATION BOX
+CRYST1   18.621   18.621   18.621  90.00  90.00  90.00 P 1           1
+MODEL       19
+ATOM      1  OW  SOL     1      15.580   9.840   2.530  1.00  0.00           O
+ATOM      2  HW1 SOL     1      14.940   9.700   1.730  1.00  0.00           H
+ATOM      3  HW2 SOL     1      16.330  10.310   2.020  1.00  0.00           H
+ATOM      4  OW  SOL     2       2.320   7.470  10.750  1.00  0.00           O
+ATOM      5  HW1 SOL     2       1.670   8.200  10.850  1.00  0.00           H
+ATOM      6  HW2 SOL     2       2.780   7.600  11.650  1.00  0.00           H
+ATOM      7  OW  SOL     3      12.570   6.410   2.170  1.00  0.00           O
+ATOM      8  HW1 SOL     3      12.000   7.260   2.360  1.00  0.00           H
+ATOM      9  HW2 SOL     3      12.780   6.300   1.220  1.00  0.00           H
+ATOM     10  OW  SOL     4       3.870  18.330   9.550  1.00  0.00           O
+ATOM     11  HW1 SOL     4       3.610  17.960  10.460  1.00  0.00           H
+ATOM     12  HW2 SOL     4       2.960  18.630   9.170  1.00  0.00           H
+ATOM     13  OW  SOL     5       2.830  11.250   9.680  1.00  0.00           O
+ATOM     14  HW1 SOL     5       2.500  12.210   9.690  1.00  0.00           H
+ATOM     15  HW2 SOL     5       2.800  11.000  10.710  1.00  0.00           H
+TER
+ENDMDL
+REMARK    GENERATED BY TRJCONV
+TITLE     water t=   0.07600 step= 380
+REMARK    THIS IS A SIMULATION BOX
+CRYST1   18.621   18.621   18.621  90.00  90.00  90.00 P 1           1
+MODEL       20
+ATOM      1  OW  SOL     1      15.560   9.840   2.520  1.00  0.00           O
+ATOM      2  HW1 SOL     1      14.920   9.650   1.750  1.00  0.00           H
+ATOM      3  HW2 SOL     1      16.300  10.390   2.020  1.00  0.00           H
+ATOM      4  OW  SOL     2       2.320   7.480  10.750  1.00  0.00           O
+ATOM      5  HW1 SOL     2       1.600   8.250  10.780  1.00  0.00           H
+ATOM      6  HW2 SOL     2       2.770   7.680  11.630  1.00  0.00           H
+ATOM      7  OW  SOL     3      12.580   6.410   2.180  1.00  0.00           O
+ATOM      8  HW1 SOL     3      12.010   7.250   2.320  1.00  0.00           H
+ATOM      9  HW2 SOL     3      12.720   6.300   1.170  1.00  0.00           H
+ATOM     10  OW  SOL     4       3.850  18.330   9.540  1.00  0.00           O
+ATOM     11  HW1 SOL     4       3.640  18.000  10.470  1.00  0.00           H
+ATOM     12  HW2 SOL     4       2.970  18.640   9.130  1.00  0.00           H
+ATOM     13  OW  SOL     5       2.800  11.260   9.680  1.00  0.00           O
+ATOM     14  HW1 SOL     5       2.560  12.230   9.660  1.00  0.00           H
+ATOM     15  HW2 SOL     5       2.860  10.990  10.630  1.00  0.00           H
+TER
+ENDMDL
+REMARK    GENERATED BY TRJCONV
+TITLE     water t=   0.08000 step= 400
+REMARK    THIS IS A SIMULATION BOX
+CRYST1   18.621   18.621   18.621  90.00  90.00  90.00 P 1           1
+MODEL       21
+ATOM      1  OW  SOL     1      15.540   9.840   2.500  1.00  0.00           O
+ATOM      2  HW1 SOL     1      14.870   9.580   1.790  1.00  0.00           H
+ATOM      3  HW2 SOL     1      16.260  10.420   2.070  1.00  0.00           H
+ATOM      4  OW  SOL     2       2.320   7.510  10.750  1.00  0.00           O
+ATOM      5  HW1 SOL     2       1.600   8.230  10.680  1.00  0.00           H
+ATOM      6  HW2 SOL     2       2.840   7.720  11.670  1.00  0.00           H
+ATOM      7  OW  SOL     3      12.590   6.410   2.190  1.00  0.00           O
+ATOM      8  HW1 SOL     3      12.010   7.210   2.270  1.00  0.00           H
+ATOM      9  HW2 SOL     3      12.650   6.300   1.200  1.00  0.00           H
+ATOM     10  OW  SOL     4       3.820  18.330   9.520  1.00  0.00           O
+ATOM     11  HW1 SOL     4       3.650  18.080  10.480  1.00  0.00           H
+ATOM     12  HW2 SOL     4       2.940  18.700   9.090  1.00  0.00           H
+ATOM     13  OW  SOL     5       2.760  11.270   9.680  1.00  0.00           O
+ATOM     14  HW1 SOL     5       2.620  12.290   9.640  1.00  0.00           H
+ATOM     15  HW2 SOL     5       2.890  10.970  10.680  1.00  0.00           H
+TER
+ENDMDL
+REMARK    GENERATED BY TRJCONV
+TITLE     water t=   0.08400 step= 420
+REMARK    THIS IS A SIMULATION BOX
+CRYST1   18.621   18.621   18.621  90.00  90.00  90.00 P 1           1
+MODEL       22
+ATOM      1  OW  SOL     1      15.530   9.830   2.480  1.00  0.00           O
+ATOM      2  HW1 SOL     1      14.810   9.520   1.790  1.00  0.00           H
+ATOM      3  HW2 SOL     1      16.240  10.420   2.050  1.00  0.00           H
+ATOM      4  OW  SOL     2       2.320   7.540  10.760  1.00  0.00           O
+ATOM      5  HW1 SOL     2       1.610   8.210  10.610  1.00  0.00           H
+ATOM      6  HW2 SOL     2       2.820   7.730  11.600  1.00  0.00           H
+ATOM      7  OW  SOL     3      12.600   6.400   2.200  1.00  0.00           O
+ATOM      8  HW1 SOL     3      11.960   7.220   2.280  1.00  0.00           H
+ATOM      9  HW2 SOL     3      12.620   6.250   1.210  1.00  0.00           H
+ATOM     10  OW  SOL     4       3.800  18.330   9.500  1.00  0.00           O
+ATOM     11  HW1 SOL     4       3.610  18.180  10.500  1.00  0.00           H
+ATOM     12  HW2 SOL     4       2.960  18.740   9.120  1.00  0.00           H
+ATOM     13  OW  SOL     5       2.740  11.280   9.680  1.00  0.00           O
+ATOM     14  HW1 SOL     5       2.700  12.290   9.660  1.00  0.00           H
+ATOM     15  HW2 SOL     5       2.850  11.020  10.670  1.00  0.00           H
+TER
+ENDMDL
+REMARK    GENERATED BY TRJCONV
+TITLE     water t=   0.08800 step= 440
+REMARK    THIS IS A SIMULATION BOX
+CRYST1   18.621   18.621   18.621  90.00  90.00  90.00 P 1           1
+MODEL       23
+ATOM      1  OW  SOL     1      15.500   9.820   2.460  1.00  0.00           O
+ATOM      2  HW1 SOL     1      14.830   9.510   1.780  1.00  0.00           H
+ATOM      3  HW2 SOL     1      16.220  10.370   1.940  1.00  0.00           H
+ATOM      4  OW  SOL     2       2.330   7.570  10.750  1.00  0.00           O
+ATOM      5  HW1 SOL     2       1.580   8.300  10.620  1.00  0.00           H
+ATOM      6  HW2 SOL     2       2.810   7.800  11.640  1.00  0.00           H
+ATOM      7  OW  SOL     3      12.600   6.410   2.210  1.00  0.00           O
+ATOM      8  HW1 SOL     3      11.960   7.170   2.320  1.00  0.00           H
+ATOM      9  HW2 SOL     3      12.650   6.160   1.200  1.00  0.00           H
+ATOM     10  OW  SOL     4       3.790  18.310   9.490  1.00  0.00           O
+ATOM     11  HW1 SOL     4       3.580  18.290  10.480  1.00  0.00           H
+ATOM     12  HW2 SOL     4       2.930  18.780   9.140  1.00  0.00           H
+ATOM     13  OW  SOL     5       2.710  11.290   9.690  1.00  0.00           O
+ATOM     14  HW1 SOL     5       2.780  12.290   9.680  1.00  0.00           H
+ATOM     15  HW2 SOL     5       2.750  11.070  10.660  1.00  0.00           H
+TER
+ENDMDL
+REMARK    GENERATED BY TRJCONV
+TITLE     water t=   0.09200 step= 460
+REMARK    THIS IS A SIMULATION BOX
+CRYST1   18.621   18.621   18.621  90.00  90.00  90.00 P 1           1
+MODEL       24
+ATOM      1  OW  SOL     1      15.480   9.810   2.440  1.00  0.00           O
+ATOM      2  HW1 SOL     1      14.810   9.510   1.730  1.00  0.00           H
+ATOM      3  HW2 SOL     1      16.170  10.250   1.830  1.00  0.00           H
+ATOM      4  OW  SOL     2       2.330   7.600  10.740  1.00  0.00           O
+ATOM      5  HW1 SOL     2       1.640   8.300  10.710  1.00  0.00           H
+ATOM      6  HW2 SOL     2       2.780   7.830  11.670  1.00  0.00           H
+ATOM      7  OW  SOL     3      12.610   6.410   2.220  1.00  0.00           O
+ATOM      8  HW1 SOL     3      11.930   7.160   2.350  1.00  0.00           H
+ATOM      9  HW2 SOL     3      12.680   6.100   1.280  1.00  0.00           H
+ATOM     10  OW  SOL     4       3.770  18.300   9.480  1.00  0.00           O
+ATOM     11  HW1 SOL     4       3.590  18.350  10.480  1.00  0.00           H
+ATOM     12  HW2 SOL     4       2.930  18.780   9.110  1.00  0.00           H
+ATOM     13  OW  SOL     5       2.690  11.290   9.690  1.00  0.00           O
+ATOM     14  HW1 SOL     5       2.860  12.310   9.660  1.00  0.00           H
+ATOM     15  HW2 SOL     5       2.630  11.070  10.730  1.00  0.00           H
+TER
+ENDMDL
+REMARK    GENERATED BY TRJCONV
+TITLE     water t=   0.09600 step= 480
+REMARK    THIS IS A SIMULATION BOX
+CRYST1   18.621   18.621   18.621  90.00  90.00  90.00 P 1           1
+MODEL       25
+ATOM      1  OW  SOL     1      15.460   9.800   2.420  1.00  0.00           O
+ATOM      2  HW1 SOL     1      14.750   9.510   1.730  1.00  0.00           H
+ATOM      3  HW2 SOL     1      16.180  10.150   1.750  1.00  0.00           H
+ATOM      4  OW  SOL     2       2.340   7.630  10.740  1.00  0.00           O
+ATOM      5  HW1 SOL     2       1.610   8.340  10.790  1.00  0.00           H
+ATOM      6  HW2 SOL     2       2.740   7.760  11.620  1.00  0.00           H
+ATOM      7  OW  SOL     3      12.610   6.400   2.240  1.00  0.00           O
+ATOM      8  HW1 SOL     3      11.920   7.170   2.290  1.00  0.00           H
+ATOM      9  HW2 SOL     3      12.710   6.090   1.270  1.00  0.00           H
+ATOM     10  OW  SOL     4       3.750  18.300   9.470  1.00  0.00           O
+ATOM     11  HW1 SOL     4       3.630  18.360  10.490  1.00  0.00           H
+ATOM     12  HW2 SOL     4       2.950  18.730   9.050  1.00  0.00           H
+ATOM     13  OW  SOL     5       2.670  11.300   9.700  1.00  0.00           O
+ATOM     14  HW1 SOL     5       2.920  12.270   9.610  1.00  0.00           H
+ATOM     15  HW2 SOL     5       2.510  11.070  10.660  1.00  0.00           H
+TER
+ENDMDL
+REMARK    GENERATED BY TRJCONV
+TITLE     water t=   0.10000 step= 500
+REMARK    THIS IS A SIMULATION BOX
+CRYST1   18.621   18.621   18.621  90.00  90.00  90.00 P 1           1
+MODEL       26
+ATOM      1  OW  SOL     1      15.450   9.780   2.380  1.00  0.00           O
+ATOM      2  HW1 SOL     1      14.660   9.520   1.790  1.00  0.00           H
+ATOM      3  HW2 SOL     1      16.200  10.060   1.740  1.00  0.00           H
+ATOM      4  OW  SOL     2       2.350   7.660  10.720  1.00  0.00           O
+ATOM      5  HW1 SOL     2       1.560   8.330  10.840  1.00  0.00           H
+ATOM      6  HW2 SOL     2       2.820   7.620  11.700  1.00  0.00           H
+ATOM      7  OW  SOL     3      12.610   6.400   2.270  1.00  0.00           O
+ATOM      8  HW1 SOL     3      11.960   7.160   2.170  1.00  0.00           H
+ATOM      9  HW2 SOL     3      12.740   6.140   1.290  1.00  0.00           H
+ATOM     10  OW  SOL     4       3.740  18.290   9.470  1.00  0.00           O
+ATOM     11  HW1 SOL     4       3.670  18.340  10.480  1.00  0.00           H
+ATOM     12  HW2 SOL     4       2.900  18.700   8.990  1.00  0.00           H
+ATOM     13  OW  SOL     5       2.650  11.310   9.710  1.00  0.00           O
+ATOM     14  HW1 SOL     5       2.960  12.260   9.600  1.00  0.00           H
+ATOM     15  HW2 SOL     5       2.400  11.090  10.670  1.00  0.00           H
+TER
+ENDMDL

diff --git a/src/testutils/simulationdatabase/spc5.top b/src/testutils/simulationdatabase/spc5.top
index 21a444c04db04a07589a1cf29745e669f907bce5..3cd42e11623d7e41cdbfaa8ae3b70dc7b29fc5a7 100644 (file)
--- a/src/testutils/simulationdatabase/spc5.top
+++ b/src/testutils/simulationdatabase/spc5.top
@@ -1,12 +1,9 @@
 #include "oplsaa.ff/forcefield.itp"
-
-; Include water topology
-#include "oplsaa.ff/tip3p.itp"
+#include "oplsaa.ff/spc.itp"
 
 [ system ]
-; Name
-spc2
+water
 
 [ molecules ]
-; Compound        #mols
-SOL              5
+sol 5
+

diff --git a/src/testutils/simulationdatabase/spc5_3.ndx b/src/testutils/simulationdatabase/spc5_3.ndx
new file mode 100644 (file)
index 0000000..1b06f91
--- /dev/null
+++ b/src/testutils/simulationdatabase/spc5_3.ndx
@@ -0,0 +1,3 @@
+[ mol ]
+1 2 3 4 5 6 10 11 12
+

diff --git a/src/testutils/simulationdatabase/spc5.gro b/src/testutils/simulationdatabase/tip3p5.gro
similarity index 100%
rename from src/testutils/simulationdatabase/spc5.gro
rename to src/testutils/simulationdatabase/tip3p5.gro

diff --git a/src/testutils/simulationdatabase/tip3p5.ndx b/src/testutils/simulationdatabase/tip3p5.ndx
new file mode 100644 (file)
index 0000000..c678461
--- /dev/null
+++ b/src/testutils/simulationdatabase/tip3p5.ndx
@@ -0,0 +1,2 @@
+[ System ]
+   1    2    3    4    5    6    7    8    9   10   11   12   13   14   15 

diff --git a/src/testutils/simulationdatabase/tip3p5.top b/src/testutils/simulationdatabase/tip3p5.top
new file mode 100644 (file)
index 0000000..20a3eb3
--- /dev/null
+++ b/src/testutils/simulationdatabase/tip3p5.top
@@ -0,0 +1,11 @@
+#include "oplsaa.ff/forcefield.itp"
+; Include water topology
+#include "oplsaa.ff/tip3p.itp"
+
+[ system ]
+; Name
+spc2
+
+[ molecules ]
+; Compound        #mols
+SOL              5