Merge branch 'release-4-5-patches' into release-4-6

Conflicts:
	src/mdlib/tpi.c

Change-Id: I1b5d92291ece7cf3194b4e1d88cd686a5aa18696

diff --cc share/top/charmm27.ff/aminoacids.rtp
Simple merge

diff --cc src/kernel/gmxcheck.c
Simple merge

diff --cc src/mdlib/domdec.c
Simple merge

diff --cc src/mdlib/edsam.c
Simple merge

diff --cc src/mdlib/pme.c
Simple merge

diff --cc src/mdlib/sim_util.c
index bf6743544041b800f1be9c05cca044848f8bbfca,047dc9d4c2b1cef66333fd09f3c2909991ca803c..e06f3d88ce411a6dcdc26d2978d30fe31491b061
--- 1/src/mdlib/sim_util.c
--- 2/src/mdlib/sim_util.c
+++ b/src/mdlib/sim_util.c
@@@ -788,17 -726,17 +788,17 @@@ void do_force(FILE *fplog,t_commrec *cr
                        cr,nrnb,wcycle,mdatoms,&(inputrec->opts),
                        x,hist,f,enerd,fcd,mtop,top,fr->born,
                        &(top->atomtypes),bBornRadii,box,
 -                      lambda,graph,&(top->excls),fr->mu_tot,
 +                      inputrec->fepvals,lambda,graph,&(top->excls),fr->mu_tot,
                        flags,&cycles_pme);
 -    
 +
      cycles_force = wallcycle_stop(wcycle,ewcFORCE);
      GMX_BARRIER(cr->mpi_comm_mygroup);
 -    
 +
      if (ed)
      {
-         do_flood(fplog,cr,x,f,ed,box,step);
+         do_flood(fplog,cr,x,f,ed,box,step,bNS);
      }
 -      
 +
      if (DOMAINDECOMP(cr))
      {
          dd_force_flop_stop(cr->dd,nrnb);

diff --cc src/mdlib/tpi.c
index 9e0fe967c6ab7f1d7662c939925ce4b5f9ff1a8b,4c2e396107c70190b99ea6b0b9c5a7f24c3b93ee..65e3fde04336ab0b28763c7ea27c64e532cc2571
--- 1/src/mdlib/tpi.c
--- 2/src/mdlib/tpi.c
+++ b/src/mdlib/tpi.c
@@@ -562,12 -566,11 +563,12 @@@ double do_tpi(FILE *fplog,t_commrec *cr
                  cr->nnodes = 1;
                  do_force(fplog,cr,inputrec,
                           step,nrnb,wcycle,top,top_global,&top_global->groups,
-                          rerun_fr.box,state->x,&state->hist,
+                          state->box,state->x,&state->hist,
                           f,force_vir,mdatoms,enerd,fcd,
 -                         lambda,NULL,fr,NULL,mu_tot,t,NULL,NULL,FALSE,
 +                         state->lambda,
 +                         NULL,fr,NULL,mu_tot,t,NULL,NULL,FALSE,
                           GMX_FORCE_NONBONDED |
-                          (bNS ? GMX_FORCE_NS | GMX_FORCE_DOLR : 0) |
+                          (bNS ? GMX_FORCE_DYNAMICBOX | GMX_FORCE_NS | GMX_FORCE_DOLR : 0) |
                           (bStateChanged ? GMX_FORCE_STATECHANGED : 0)); 
                  cr->nnodes = nnodes;
                  bStateChanged = FALSE;

diff --cc src/tools/gmx_energy.c
index 52ec7ffbd14d7aff53e061a015647f3a2aa4cbb7,7931b808839aaaccbceb01acd79bd782fb3592f5..83c00bf2a718afb8a1ac562dd21b997f33d42e61
--- 1/src/tools/gmx_energy.c
--- 2/src/tools/gmx_energy.c
+++ b/src/tools/gmx_energy.c
@@@ -1604,9 -1658,10 +1604,10 @@@ int gmx_energy(int argc,char *argv[]
      "energy values.[PAR]",
  
      "The term fluctuation gives the RMSD around the least-squares fit.[PAR]",
 -    
 +
      "Some fluctuation-dependent properties can be calculated provided",
-     "the correct energy terms are selected. The following properties",
+     "the correct energy terms are selected, and that the command line option",
+     "[TT]-fluct_props[tt] is given. The following properties",
      "will be computed:[BR]",
      "Property                        Energy terms needed[BR]",
      "---------------------------------------------------[BR]",
@@@ -1667,10 -1722,10 +1668,10 @@@
      "files, and the average is over the ensemble A. The running average",
      "of the free energy difference is printed to a file specified by [TT]-ravg[tt].",
      "[BB]Note[bb] that the energies must both be calculated from the same trajectory."
 -    
 +
    };
    static gmx_bool bSum=FALSE,bFee=FALSE,bPrAll=FALSE,bFluct=FALSE,bDriftCorr=FALSE;
-   static gmx_bool bDp=FALSE,bMutot=FALSE,bOrinst=FALSE,bOvec=FALSE;
+   static gmx_bool bDp=FALSE,bMutot=FALSE,bOrinst=FALSE,bOvec=FALSE,bFluctProps=FALSE;
    static int  skip=0,nmol=1,nbmin=5,nbmax=5;
    static real reftemp=300.0,ezero=0;
    t_pargs pa[] = {
@@@ -2420,11 -2487,12 +2423,12 @@@
                     time,reftemp,&edat,
                     nset,set,bIsEner,leg,enm,Vaver,ezero,nbmin,nbmax,
                     oenv);
-       calc_fluctuation_props(stdout,bDriftCorr,dt,nset,set,nmol,leg,&edat,
-                              nbmin,nbmax);
+       if (bFluctProps)
+           calc_fluctuation_props(stdout,bDriftCorr,dt,nset,set,nmol,leg,&edat,
+                                  nbmin,nbmax);
    }
    if (opt2bSet("-f2",NFILE,fnm)) {
 -      fec(opt2fn("-f2",NFILE,fnm), opt2fn("-ravg",NFILE,fnm), 
 +      fec(opt2fn("-f2",NFILE,fnm), opt2fn("-ravg",NFILE,fnm),
            reftemp, nset, set, leg, &edat, time ,oenv);
    }
  

diff --cc src/tools/gmx_trjconv.c
Simple merge

diff --cc src/tools/make_edi.c
Simple merge