Merge "Adapted NMR related data to new pdb format." into release-4-5-patches

diff --git a/src/gmxlib/copyrite.c b/src/gmxlib/copyrite.c
index 48267b802710165b097675bea391acb608ec0deb..d01a9c0a1b741bea7298f8785c44ca0b43a199f8 100644 (file)
--- a/src/gmxlib/copyrite.c
+++ b/src/gmxlib/copyrite.c
@@ -528,7 +528,12 @@ void please_cite(FILE *fp,const char *key)
       "Optimizing working parameters of the smooth particle mesh Ewald algorithm in terms of accuracy and efficiency",
       "J. Chem. Phys. B",
       133, 2010, "034117"
-    }
+    },
+    { "Sugita1999a",
+      "Y. Sugita, Y. Okamoto",
+      "Replica-exchange molecular dynamics method for protein folding",
+      "Chem. Phys. Lett.",
+      314, 1999, "141-151" },
   };
 #define NSTR (int)asize(citedb)
   

diff --git a/src/kernel/readir.c b/src/kernel/readir.c
index 18c3c18a2b5920d90e6726a48c587ef3a06e661a..8163d9275b2e520f156d5619d6f9dbe137f652d0 100644 (file)
--- a/src/kernel/readir.c
+++ b/src/kernel/readir.c
@@ -434,16 +434,17 @@ void check_ir(const char *mdparin,t_inputrec *ir, t_gromppopts *opts,
         sprintf(err_buf,"pressure coupling with PPPM not implemented, use PME");
         CHECK(ir->coulombtype == eelPPPM);
 
-        if (epcPARRINELLORAHMAN == ir->epct && opts->bGenVel)
+        if (epcPARRINELLORAHMAN == ir->epc && opts->bGenVel)
         {
             sprintf(warn_buf,
                     "You are generating velocities so I am assuming you "
                     "are equilibrating a system. You are using "
-                    "Parrinello-Rahman pressure coupling, but this can be "
+                    "%s pressure coupling, but this can be "
                     "unstable for equilibration. If your system crashes, try "
                     "equilibrating first with Berendsen pressure coupling. If "
                     "you are not equilibrating the system, you can probably "
-                    "ignore this warning.");
+                    "ignore this warning.",
+                    epcoupl_names[ir->epc]);
             warning(wi,warn_buf);
         }
     }

diff --git a/src/kernel/repl_ex.c b/src/kernel/repl_ex.c
index e4c9089951c62f79243f1fbe8bb500b11e26158f..2ec6f533726be7ab1cc1cc42ca18332cd30b1aa6 100644 (file)
--- a/src/kernel/repl_ex.c
+++ b/src/kernel/repl_ex.c
@@ -180,7 +180,7 @@ gmx_repl_ex_t init_replica_exchange(FILE *fplog,
     switch (re->type)
     {
     case ereTEMP:
-        please_cite(fplog,"Hukushima96a");
+        please_cite(fplog,"Sugita1999a");
         if (ir->epc != epcNO)
         {
             re->bNPT = TRUE;

diff --git a/src/kernel/runner.c b/src/kernel/runner.c
index b215a8409fb3c32c85d7052fd170266c2c48d7c2..23e3a7620227ac6d3dbc94bcd20706d1e49e072f 100644 (file)
--- a/src/kernel/runner.c
+++ b/src/kernel/runner.c
@@ -427,6 +427,12 @@ int mdrunner(int nthreads_requested, FILE *fplog,t_commrec *cr,int nfile,
     /* now make sure the state is initialized and propagated */
     set_state_entries(state,inputrec,cr->nnodes);
 
+    /* remove when vv and rerun works correctly! */
+    if (PAR(cr) && EI_VV(inputrec->eI) && ((Flags & MD_RERUN) || (Flags & MD_RERUN_VSITE)))
+    {
+        gmx_fatal(FARGS, "Currently can't do velocity verlet with rerun in parallel.");
+    }
+
     /* A parallel command line option consistency check that we can
        only do after any threads have started. */
     if (!PAR(cr) &&