Merge branch release-5-1 into release-2016

Trivial conflicts in minimize.cpp from bug fix in same region that now
has exceptions caught within an OpenMP region.

Change-Id: I8b3c269a2afd7d4967e0f7310c96af6022533ddd

diff --git a/share/top/amber03.ff/aminoacids.rtp b/share/top/amber03.ff/aminoacids.rtp
index 0c36f000cc12d8e323be7f338f88c38d8b9f4406..1288d1d1997a2e1addf91c94c15e3b025d14d3b5 100644 (file)
--- a/share/top/amber03.ff/aminoacids.rtp
+++ b/share/top/amber03.ff/aminoacids.rtp
@@ -644,24 +644,24 @@
                         
 [ HIP ]
  [ atoms ]
-     N    N           -0.150599    1
-     H    H            0.174903    2
-    CA    CT          -0.139355    3
-    HA    H1           0.103647    4
-    CB    CT          -0.105724    5
-   HB1    HC           0.102146    6
-   HB2    HC           0.102146    7
-    CG    CC           0.051128    8
-   ND1    NA           0.002100    9
-   HD1    H            0.258443   10
-   CE1    CR          -0.033333   11
-   HE1    H5           0.218884   12
-   NE2    NA          -0.140978   13
-   HE2    H            0.353373   14
-   CD2    CW          -0.143848   15
-   HD2    H4           0.213519   16
-     C    C            0.675645   17
-     O    O           -0.542097   18
+     N    N           -0.424967    1
+     H    H            0.285872    2
+    CA    CT           0.375022    3
+    HA    H1          -0.014621    4
+    CB    CT          -0.332123    5
+   HB1    HC           0.107725    6
+   HB2    HC           0.107725    7
+    CG    CC           0.182399    8
+   ND1    NA          -0.087602    9
+   HD1    H            0.305096   10
+   CE1    CR          -0.013105   11
+   HE1    H5           0.230635   12
+   NE2    NA          -0.148766   13
+   HE2    H            0.377295   14
+   CD2    CW          -0.192052   15
+   HD2    H4           0.235237   16
+     C    C            0.566646   17
+     O    O           -0.560417   18
  [ bonds ]
      N     H
      N    CA
@@ -1072,27 +1072,27 @@
 
 [ LYN ]
  [ atoms ]
-     N    N           -0.415700    1
-     H    H            0.271900    2
-    CA    CT          -0.072060    3
-    HA    H1           0.099400    4
-    CB    CT          -0.048450    5
-   HB1    HC           0.034000    6
-   HB2    HC           0.034000    7
-    CG    CT           0.066120    8
-   HG1    HC           0.010410    9
-   HG2    HC           0.010410   10
-    CD    CT          -0.037680   11
-   HD1    HC           0.011550   12
-   HD2    HC           0.011550   13
-    CE    CT           0.326040   14
-   HE1    HP          -0.033580   15
-   HE2    HP          -0.033580   16
-    NZ    N3          -1.035810   17
-   HZ1    H            0.386040   18
-   HZ2    H            0.386040   19
-     C    C            0.597300   20
-     O    O           -0.567900   21
+     N    N           -0.453388    1
+     H    H            0.289695    2
+    CA    CT          -0.024500    3
+    HA    H1           0.099553    4
+    CB    CT           0.035478    5
+   HB1    HC           0.004797    6
+   HB2    HC           0.004797    7
+    CG    CT          -0.019962    8
+   HG1    HC          -0.015610    9
+   HG2    HC          -0.015610   10
+    CD    CT           0.041105   11
+   HD1    HC           0.008304   12
+   HD2    HC           0.008304   13
+    CE    CT           0.188382   14
+   HE1    HP           0.016810   15
+   HE2    HP           0.016810   16
+    NZ    N3          -0.894254   17
+   HZ1    H            0.332053   18
+   HZ2    H            0.332053   19
+     C    C            0.608464   20
+     O    O           -0.563281   21
  [ bonds ]
      N     H
      N    CA

diff --git a/share/top/charmm27.ff/aminoacids.hdb b/share/top/charmm27.ff/aminoacids.hdb
index 7a9a4ea0a116c99b903c659d6bde4530e19f785e..4775ad7989216799e30e2559a51a73fe2a6801fc 100644 (file)
--- a/share/top/charmm27.ff/aminoacids.hdb
+++ b/share/top/charmm27.ff/aminoacids.hdb
@@ -72,13 +72,6 @@ GLUP    5
 GLY     2       
 1      1       HN      N       -C      CA
 2      6       HA      CA      C       N
-HIS1    6       
-1      1       HN      N       -C      CA
-1      5       HA      CA      N       C       CB
-2      6       HB      CB      CG      CA
-1      1       HD2     CD2     CG      NE2
-1      1       HE1     CE1     ND1     NE2
-1      1       HD1     ND1     CG      CE1
 HSD     6       
 1      1       HN      N       -C      CA
 1      5       HA      CA      N       C       CB

diff --git a/share/top/oplsaa.ff/aminoacids.hdb b/share/top/oplsaa.ff/aminoacids.hdb
index a7d8b1d72c02ba6f51159e7b138838599cef5aa3..5d2205fb3b58a694e7499fa005b2a96f19e99735 100644 (file)
--- a/share/top/oplsaa.ff/aminoacids.hdb
+++ b/share/top/oplsaa.ff/aminoacids.hdb
@@ -81,13 +81,6 @@ GLUH    5
 GLY     2       
 1      1       H       N       -C      CA
 2      6       HA      CA      C       N
-HIS1    6       
-1      1       H       N       -C      CA
-1      5       HA      CA      N       C       CB
-2      6       HB      CB      CG      CA
-1      1       HD2     CD2     CG      NE2
-1      1       HE1     CE1     ND1     NE2
-1      1       HD1     ND1     CG      CE1
 HISD    6       
 1      1       H       N       -C      CA
 1      5       HA      CA      N       C       CB

diff --git a/share/top/oplsaa.ff/aminoacids.rtp b/share/top/oplsaa.ff/aminoacids.rtp
index c59c1d6118df12517b237531acac6dd87cf0bee6..65c01723e901b89767589a794a9671ee3cc3f50b 100644 (file)
--- a/share/top/oplsaa.ff/aminoacids.rtp
+++ b/share/top/oplsaa.ff/aminoacids.rtp
@@ -715,57 +715,6 @@
    ND1   NE2   CE1   HE1    improper_Z_CA_X_Y 
 
 
-[ HIS1 ]   ; Identical to HISD
- [ atoms ]
-     N    opls_238   -0.500     1
-     H    opls_241    0.300     1
-    CA    opls_224B   0.140     1
-    HA    opls_140    0.060     1
-    CB    opls_505   -0.297     2 
-   HB1    opls_140    0.060     2 
-   HB2    opls_140    0.060     2 
-    CG    opls_508   -0.261     3
-   ND1    opls_503   -0.291     4
-   HD1    opls_504    0.326     4
-   CD2    opls_507    0.504     5
-   HD2    opls_146    0.183     5
-   CE1    opls_506    0.182     6
-   HE1    opls_146    0.098     6
-   NE2    opls_511   -0.564     7
-     C    opls_235    0.500     8
-     O    opls_236   -0.500     8
- [ bonds ]
-     N     H
-     N    CA
-    CA    HA
-    CA    CB
-    CA     C
-    CB   HB1
-    CB   HB2
-    CB    CG
-    CG   ND1
-    CG   CD2
-   ND1   HD1
-   ND1   CE1
-   CD2   HD2
-   CD2   NE2
-   CE1   HE1
-   CE1   NE2
-     C     O
-    -C     N
- [ dihedrals ] ; override some with residue-specific ones
-     N    CA    CB    CG    dih_HIS_chi1_N_C_C_C
-    CG    CB    CA     C    dih_HIS_chi1_C_C_C_CO
-    CA    CB    CG   ND1    dih_HIS_chi2_C_C_C_N
- [ impropers ]
-    -C    CA     N     H    improper_Z_N_X_Y  
-    CA    +N     C     O    improper_O_C_X_Y  
-   ND1   CD2    CG    CB    improper_Z_CA_X_Y 
-    CG   CE1   ND1   HD1    improper_Z_N_X_Y  
-    CG   NE2   CD2   HD2    improper_Z_CA_X_Y 
-   ND1   NE2   CE1   HE1    improper_Z_CA_X_Y 
-
-
 [ HISE ] 
  [ atoms ]
      N    opls_238   -0.500     1

diff --git a/src/gromacs/mdlib/minimize.cpp b/src/gromacs/mdlib/minimize.cpp
index 591e20a7dc88cbfa338f971b35b97ed014b2a718..2d5290d4b9502a9d1f900089717a5b1578c490ed 100644 (file)
--- a/src/gromacs/mdlib/minimize.cpp
+++ b/src/gromacs/mdlib/minimize.cpp
@@ -580,9 +580,7 @@ static bool do_em_step(t_commrec *cr, t_inputrec *ir, t_mdatoms *md,
 
 {
     t_state *s1, *s2;
-    int      i;
     int      start, end;
-    rvec    *x1, *x2;
     real     dvdl_constr;
     int      nthreads gmx_unused;
 
@@ -615,7 +613,7 @@ static bool do_em_step(t_commrec *cr, t_inputrec *ir, t_mdatoms *md,
     s2->natoms = s1->natoms;
     copy_mat(s1->box, s2->box);
     /* Copy free energy state */
-    for (i = 0; i < efptNR; i++)
+    for (int i = 0; i < efptNR; i++)
     {
         s2->lambda[i] = s1->lambda[i];
     }
@@ -624,18 +622,16 @@ static bool do_em_step(t_commrec *cr, t_inputrec *ir, t_mdatoms *md,
     start = 0;
     end   = md->homenr;
 
-    x1 = s1->x;
-    x2 = s2->x;
-
     // cppcheck-suppress unreadVariable
     nthreads = gmx_omp_nthreads_get(emntUpdate);
 #pragma omp parallel num_threads(nthreads)
     {
-        int gf, i, m;
+        rvec *x1 = s1->x;
+        rvec *x2 = s2->x;
 
-        gf = 0;
+        int   gf = 0;
 #pragma omp for schedule(static) nowait
-        for (i = start; i < end; i++)
+        for (int i = start; i < end; i++)
         {
             try
             {
@@ -643,7 +639,7 @@ static bool do_em_step(t_commrec *cr, t_inputrec *ir, t_mdatoms *md,
                 {
                     gf = md->cFREEZE[i];
                 }
-                for (m = 0; m < DIM; m++)
+                for (int m = 0; m < DIM; m++)
                 {
                     if (ir->opts.nFreeze[gf][m])
                     {
@@ -661,13 +657,13 @@ static bool do_em_step(t_commrec *cr, t_inputrec *ir, t_mdatoms *md,
         if (s2->flags & (1<<estCGP))
         {
             /* Copy the CG p vector */
-            x1 = s1->cg_p;
-            x2 = s2->cg_p;
+            rvec *p1 = s1->cg_p;
+            rvec *p2 = s2->cg_p;
 #pragma omp for schedule(static) nowait
-            for (i = start; i < end; i++)
+            for (int i = start; i < end; i++)
             {
                 // Trivial OpenMP block that does not throw
-                copy_rvec(x1[i], x2[i]);
+                copy_rvec(p1[i], p2[i]);
             }
         }
 
@@ -690,7 +686,7 @@ static bool do_em_step(t_commrec *cr, t_inputrec *ir, t_mdatoms *md,
             }
             s2->ncg_gl = s1->ncg_gl;
 #pragma omp for schedule(static) nowait
-            for (i = 0; i < s2->ncg_gl; i++)
+            for (int i = 0; i < s2->ncg_gl; i++)
             {
                 s2->cg_gl[i] = s1->cg_gl[i];
             }