Storing gromacs 4.6.3 diff with original files

patches/gromacs-4.6.3.diff

-patch -u -l -b -F 5 --suffix=.preplumed "./src/kernel/CMakeLists.txt" << \EOF_EOF
---- ./src/kernel/CMakeLists.txt.preplumed
-+++ ./src/kernel/CMakeLists.txt
-@@ -31,10 +31,12 @@
- #
- # To help us fund GROMACS development, we humbly ask that you cite
- # the research papers on the package. Check out http://www.gromacs.org.
- #
- 
-+include(${CMAKE_SOURCE_DIR}/Plumed.cmake)
-+
- set(GMXPREPROCESS_SOURCES 
-     add_par.c       
-     calc_verletbuf.c
-     compute_io.c    
-     convparm.c      
-@@ -121,11 +123,11 @@
-     set_target_properties(${PROGRAM} PROPERTIES OUTPUT_NAME "${PROGRAM}${GMX_BINARY_SUFFIX}")
- endforeach()
- 
- add_executable(mdrun ${MDRUN_SOURCES} main.c)
- gmx_add_man_page(mdrun)
--target_link_libraries(mdrun gmxpreprocess md gmx ${OpenMP_LINKER_FLAGS})
-+target_link_libraries(mdrun gmxpreprocess md gmx ${OpenMP_LINKER_FLAGS} ${PLUMED_LOAD})
- set_target_properties(mdrun PROPERTIES OUTPUT_NAME "mdrun${GMX_BINARY_SUFFIX}" COMPILE_FLAGS "${OpenMP_C_FLAGS}")
- 
- if(GMX_OPENMM)
-     target_link_libraries(mdrun openmm_api_wrapper)
- endif()
-EOF_EOF
-patch -u -l -b -F 5 --suffix=.preplumed "./src/kernel/md.c" << \EOF_EOF
---- ./src/kernel/md.c.preplumed
-+++ ./src/kernel/md.c
-@@ -91,10 +91,16 @@
- #include "membed.h"
- #include "types/nlistheuristics.h"
- #include "types/iteratedconstraints.h"
- #include "nbnxn_cuda_data_mgmt.h"
- 
-+/* PLUMED */
-+#include "../../Plumed.h"
-+extern int    plumedswitch;
-+extern plumed plumedmain;
-+/* END PLUMED */
-+
- #ifdef GMX_LIB_MPI
- #include <mpi.h>
- #endif
- #ifdef GMX_THREAD_MPI
- #include "tmpi.h"
-@@ -235,10 +241,14 @@
-     /* PME load balancing data for GPU kernels */
-     pme_load_balancing_t pme_loadbal = NULL;
-     double               cycles_pmes;
-     gmx_bool             bPMETuneTry = FALSE, bPMETuneRunning = FALSE;
- 
-+/* PLUMED */
-+    int plumedNeedsEnergy;
-+/* END PLUMED */
-+
- #ifdef GMX_FAHCORE
-     /* Temporary addition for FAHCORE checkpointing */
-     int chkpt_ret;
- #endif
- 
-@@ -715,10 +725,50 @@
-             }
-         }
-         fprintf(fplog, "\n");
-     }
- 
-+    /* PLUMED */
-+    if(plumedswitch){
-+      if(cr->ms && cr->ms->nsim>1) {
-+        if(MASTER(cr)) plumed_cmd(plumedmain,"GREX setMPIIntercomm",&cr->ms->mpi_comm_masters);
-+        if(PAR(cr)){
-+          if(DOMAINDECOMP(cr)) {
-+            plumed_cmd(plumedmain,"GREX setMPIIntracomm",&cr->dd->mpi_comm_all);
-+          }else{
-+            plumed_cmd(plumedmain,"GREX setMPIIntracomm",&cr->mpi_comm_mysim);
-+          }
-+        }
-+        plumed_cmd(plumedmain,"GREX init",NULL);
-+      }
-+      if(PAR(cr)){
-+        if(DOMAINDECOMP(cr)) {
-+          plumed_cmd(plumedmain,"setMPIComm",&cr->dd->mpi_comm_all);
-+        }else{
-+          plumed_cmd(plumedmain,"setMPIComm",&cr->mpi_comm_mysim);
-+        }
-+      }
-+      plumed_cmd(plumedmain,"setNatoms",&top_global->natoms);
-+      plumed_cmd(plumedmain,"setMDEngine","gromacs");
-+      plumed_cmd(plumedmain,"setLog",fplog);
-+      real real_delta_t;
-+      real_delta_t=ir->delta_t;
-+      plumed_cmd(plumedmain,"setTimestep",&real_delta_t);
-+      plumed_cmd(plumedmain,"init",NULL);
-+
-+      if(PAR(cr)){
-+        if(DOMAINDECOMP(cr)) {
-+          plumed_cmd(plumedmain,"setAtomsNlocal",&cr->dd->nat_home);
-+          plumed_cmd(plumedmain,"setAtomsGatindex",cr->dd->gatindex);
-+        }else{
-+          plumed_cmd(plumedmain,"setAtomsNlocal",&mdatoms->homenr);
-+          plumed_cmd(plumedmain,"setAtomsContiguous",&mdatoms->start);
-+        }
-+      }
-+    }
-+    /* END PLUMED */
-+
-     /* Set and write start time */
-     runtime_start(runtime);
-     print_date_and_time(fplog, cr->nodeid, "Started mdrun", runtime);
-     wallcycle_start(wcycle, ewcRUN);
-     if (fplog)
-@@ -1031,10 +1081,17 @@
-                                     vsite, shellfc, constr,
-                                     nrnb, wcycle,
-                                     do_verbose && !bPMETuneRunning);
-                 wallcycle_stop(wcycle, ewcDOMDEC);
-                 /* If using an iterative integrator, reallocate space to match the decomposition */
-+
-+                /* PLUMED */
-+                if(plumedswitch){
-+                  plumed_cmd(plumedmain,"setAtomsNlocal",&cr->dd->nat_home);
-+                  plumed_cmd(plumedmain,"setAtomsGatindex",cr->dd->gatindex);
-+                }
-+                /* END PLUMED */
-             }
-         }
- 
-         if (MASTER(cr) && do_log && !bFFscan)
-         {
-@@ -1176,16 +1233,39 @@
-             /* The coordinates (x) are shifted (to get whole molecules)
-              * in do_force.
-              * This is parallellized as well, and does communication too.
-              * Check comments in sim_util.c
-              */
-+ 
-+            /* PLUMED */
-+            plumedNeedsEnergy=0;
-+            if(plumedswitch){
-+              long int lstep=step; plumed_cmd(plumedmain,"setStepLong",&lstep);
-+              plumed_cmd(plumedmain,"setPositions",&state->x[mdatoms->start][0]);
-+              plumed_cmd(plumedmain,"setMasses",&mdatoms->massT[mdatoms->start]);
-+              plumed_cmd(plumedmain,"setCharges",&mdatoms->chargeA[mdatoms->start]);
-+              plumed_cmd(plumedmain,"setBox",&state->box[0][0]);
-+              plumed_cmd(plumedmain,"prepareCalc",NULL);
-+              plumed_cmd(plumedmain,"isEnergyNeeded",&plumedNeedsEnergy);
-+            }
-+            /* END PLUMED */
-             do_force(fplog, cr, ir, step, nrnb, wcycle, top, top_global, groups,
-                      state->box, state->x, &state->hist,
-                      f, force_vir, mdatoms, enerd, fcd,
-                      state->lambda, graph,
-                      fr, vsite, mu_tot, t, outf->fp_field, ed, bBornRadii,
--                     (bNS ? GMX_FORCE_NS : 0) | force_flags);
-+                     (plumedNeedsEnergy? GMX_FORCE_ENERGY : 0) |(bNS ? GMX_FORCE_NS : 0) | force_flags);
-+            /* PLUMED */
-+            if(plumedswitch){
-+              if(plumedNeedsEnergy) plumed_cmd(plumedmain,"setEnergy",&enerd->term[F_EPOT]);
-+              plumed_cmd(plumedmain,"setForces",&f[mdatoms->start][0]);
-+              plumed_cmd(plumedmain,"setVirial",&force_vir[0][0]);
-+              plumed_cmd(plumedmain,"performCalc",NULL);
-+              if ((repl_ex_nst > 0) && (step > 0) && !bLastStep &&
-+                 do_per_step(step,repl_ex_nst)) plumed_cmd(plumedmain,"GREX savePositions",NULL);
-+            }
-+            /* END PLUMED */
-         }
- 
-         GMX_BARRIER(cr->mpi_comm_mygroup);
- 
-         if (bTCR)
-EOF_EOF
-patch -u -l -b -F 5 --suffix=.preplumed "./src/kernel/mdrun.c" << \EOF_EOF
---- ./src/kernel/mdrun.c.preplumed
-+++ ./src/kernel/mdrun.c
-@@ -56,10 +56,16 @@
- #endif
- 
- /* afm stuf */
- #include "pull.h"
- 
-+/* PLUMED */
-+#include "../../Plumed.h"
-+int    plumedswitch;
-+plumed plumedmain;
-+/* END PLUMED */
-+
- int cmain(int argc, char *argv[])
- {
-     const char   *desc[] = {
-         "The [TT]mdrun[tt] program is the main computational chemistry engine",
-         "within GROMACS. Obviously, it performs Molecular Dynamics simulations,",
-@@ -399,10 +405,11 @@
-         { efLOG, "-rs",     "rotslabs", ffOPTWR },
-         { efLOG, "-rt",     "rottorque", ffOPTWR },
-         { efMTX, "-mtx",    "nm",       ffOPTWR },
-         { efNDX, "-dn",     "dipole",   ffOPTWR },
-         { efRND, "-multidir", NULL,      ffOPTRDMULT},
-+        { efDAT, "-plumed", "plumed",   ffOPTRD },   /* PLUMED */
-         { efDAT, "-membed", "membed",   ffOPTRD },
-         { efTOP, "-mp",     "membed",   ffOPTRD },
-         { efNDX, "-mn",     "membed",   ffOPTRD }
-     };
- #define NFILE asize(fnm)
-@@ -731,19 +738,50 @@
-     }
- 
-     ddxyz[XX] = (int)(realddxyz[XX] + 0.5);
-     ddxyz[YY] = (int)(realddxyz[YY] + 0.5);
-     ddxyz[ZZ] = (int)(realddxyz[ZZ] + 0.5);
-+    /* PLUMED */
-+    plumedswitch=0;
-+    if (opt2bSet("-plumed",NFILE,fnm)) plumedswitch=1;
-+    if(plumedswitch){
-+      int plumed_is_there=0;
-+      int real_precision=sizeof(real);
-+      real energyUnits=1.0;
-+      real lengthUnits=1.0;
-+      real timeUnits=1.0;
-+  
-+  
-+      if(!plumed_installed()){
-+        gmx_fatal(FARGS,"Plumed is not available. Check your PLUMED_KERNEL variable.");
-+      }
-+      plumedmain=plumed_create();
-+      plumed_cmd(plumedmain,"setRealPrecision",&real_precision);
-+      // this is not necessary for gromacs units:
-+      plumed_cmd(plumedmain,"setMDEnergyUnits",&energyUnits);
-+      plumed_cmd(plumedmain,"setMDLengthUnits",&lengthUnits);
-+      plumed_cmd(plumedmain,"setMDTimeUnits",&timeUnits);
-+      //
-+      plumed_cmd(plumedmain,"setPlumedDat",ftp2fn(efDAT,NFILE,fnm));
-+      plumedswitch=1;
-+    }
-+    /* END PLUMED */
- 
-     rc = mdrunner(&hw_opt, fplog, cr, NFILE, fnm, oenv, bVerbose, bCompact,
-                   nstglobalcomm, ddxyz, dd_node_order, rdd, rconstr,
-                   dddlb_opt[0], dlb_scale, ddcsx, ddcsy, ddcsz,
-                   nbpu_opt[0],
-                   nsteps, nstepout, resetstep,
-                   nmultisim, repl_ex_nst, repl_ex_nex, repl_ex_seed,
-                   pforce, cpt_period, max_hours, deviceOptions, Flags);
- 
-+    /* PLUMED */
-+    if(plumedswitch){
-+      plumed_finalize(plumedmain);
-+    }
-+    /* END PLUMED */
-+  
-     gmx_finalize_par();
- 
-     if (MULTIMASTER(cr))
-     {
-         thanx(stderr);
-EOF_EOF
-patch -u -l -b -F 5 --suffix=.preplumed "./src/kernel/repl_ex.c" << \EOF_EOF
---- ./src/kernel/repl_ex.c.preplumed
-+++ ./src/kernel/repl_ex.c
-@@ -51,10 +51,16 @@
- #include "names.h"
- #include "mvdata.h"
- #include "domdec.h"
- #include "partdec.h"
- 
-+/* PLUMED */
-+#include "../../Plumed.h"
-+extern int    plumedswitch;
-+extern plumed plumedmain;
-+/* END PLUMED */
-+
- #define PROBABILITYCUTOFF 100
- /* we don't bother evaluating if events are more rare than exp(-100) = 3.7x10^-44 */
- 
- enum {
-     ereTEMP, ereLAMBDA, ereENDSINGLE, ereTL, ereNR
-@@ -111,18 +117,20 @@
- 
-     snew(qall, ms->nsim);
-     qall[re->repl] = q;
-     gmx_sum_sim(ms->nsim, qall, ms);
- 
--    bDiff = FALSE;
--    for (s = 1; s < ms->nsim; s++)
--    {
--        if (qall[s] != qall[0])
--        {
-+    /* PLUMED */
-+    //bDiff = FALSE;
-+    //for (s = 1; s < ms->nsim; s++)
-+    //{
-+    //    if (qall[s] != qall[0])
-+    //    {
-             bDiff = TRUE;
--        }
--    }
-+    //    }
-+    //}
-+    /* END PLUMED */
- 
-     if (bDiff)
-     {
-         /* Set the replica exchange type and quantities */
-         re->type = ere;
-@@ -255,10 +263,14 @@
-     for (i = 0; i < re->nrepl; i++)
-     {
-         re->ind[i] = i;
-     }
- 
-+    /* PLUMED */
-+    // plumed2: check if we want alternative patterns (i.e. for bias-exchange metaD)
-+    // in those cases replicas can share the same temperature.
-+    /*
-     if (re->type < ereENDSINGLE)
-     {
- 
-         for (i = 0; i < re->nrepl; i++)
-         {
-@@ -275,10 +287,12 @@
-                     gmx_fatal(FARGS, "Two replicas have identical %ss", erename[re->type]);
-                 }
-             }
-         }
-     }
-+    */
-+    /* END PLUMED */
- 
-     /* keep track of all the swaps, starting with the initial placement. */
-     snew(re->allswaps, re->nrepl);
-     for (i = 0; i < re->nrepl; i++)
-     {
-@@ -976,10 +990,14 @@
-     for (i = 0; i < re->nrepl; i++)
-     {
-         pind[i] = re->ind[i];
-     }
- 
-+    /* PLUMED */
-+    int plumed_test_exchange_pattern=0;
-+    /* END PLUMED */
-+
-     if (bMultiEx)
-     {
-         /* multiple random switch exchange */
-         for (i = 0; i < re->nex; i++)
-         {
-@@ -1045,19 +1063,56 @@
-     }
-     else
-     {
-         /* standard nearest neighbor replica exchange */
-         m = (step / re->nst) % 2;
-+        /* PLUMED */
-+        if(plumedswitch){
-+          int partner=re->repl;
-+          plumed_cmd(plumedmain,"getExchangesFlag",&plumed_test_exchange_pattern);
-+          if(plumed_test_exchange_pattern>0){
-+            int *list;
-+            snew(list,re->nrepl);
-+            plumed_cmd(plumedmain,"setNumberOfReplicas",&(re->nrepl));
-+            plumed_cmd(plumedmain,"getExchangesList",list);
-+            for(i=0; i<re->nrepl; i++) re->ind[i]=list[i];
-+            sfree(list);
-+          }
-+
-+          for(i=1; i<re->nrepl; i++) {
-+            if (i % 2 != m) continue;
-+            a = re->ind[i-1];
-+            b = re->ind[i];
-+            if(re->repl==a) partner=b;
-+            if(re->repl==b) partner=a;
-+          }
-+          plumed_cmd(plumedmain,"GREX setPartner",&partner);
-+          plumed_cmd(plumedmain,"GREX calculate",NULL);
-+          plumed_cmd(plumedmain,"GREX shareAllDeltaBias",NULL);
-+        }
-+        /* END PLUMED */
-         for (i = 1; i < re->nrepl; i++)
-         {
-             a = re->ind[i-1];
-             b = re->ind[i];
- 
-             bPrint = (re->repl == a || re->repl == b);
-             if (i % 2 == m)
-             {
-                 delta = calc_delta(fplog, bPrint, re, a, b, a, b);
-+                /* PLUMED */
-+                if(plumedswitch){
-+                  real adb,bdb,dplumed;
-+                  char buf[300];
-+                  sprintf(buf,"GREX getDeltaBias %d",a); plumed_cmd(plumedmain,buf,&adb);
-+                  sprintf(buf,"GREX getDeltaBias %d",b); plumed_cmd(plumedmain,buf,&bdb);
-+                  dplumed=adb*re->beta[a]+bdb*re->beta[b];
-+                  delta+=dplumed;
-+                  if (bPrint)
-+                    fprintf(fplog,"dplumed = %10.3e  dE_Term = %10.3e (kT)\n",dplumed,delta);
-+                }
-+                /* END PLUMED */
-                 if (delta <= 0)
-                 {
-                     /* accepted */
-                     prob[i] = 1;
-                     bEx[i]  = TRUE;
-@@ -1077,15 +1132,26 @@
-                 }
-                 re->prob_sum[i] += prob[i];
- 
-                 if (bEx[i])
-                 {
-+                  /* PLUMED */
-+                  if(!plumed_test_exchange_pattern) {
-+                    /* standard neighbour swapping */
-                     /* swap these two */
-                     tmp       = pind[i-1];
-                     pind[i-1] = pind[i];
-                     pind[i]   = tmp;
-                     re->nexchange[i]++;  /* statistics for back compatibility */
-+                  } else {
-+                    /* alternative swapping patterns */
-+                    tmp       = pind[a];
-+                    pind[a]   = pind[b];
-+                    pind[b]   = tmp;
-+                    re->nexchange[i]++;  /* statistics for back compatibility */
-+                  }
-+                  /* END PLUMED */
-                 }
-             }
-             else
-             {
-                 prob[i] = -1;
-@@ -1097,10 +1163,19 @@
-         print_prob(fplog, "pr", re->nrepl, prob);
-         fprintf(fplog, "\n");
-         re->nattempt[m]++;
-     }
- 
-+    /* PLUMED */
-+    if(plumed_test_exchange_pattern>0) {
-+      for (i = 0; i < re->nrepl; i++)
-+      {
-+          re->ind[i] = i;
-+      }
-+    }
-+    /* END PLUMED */
-+
-     /* record which moves were made and accepted */
-     for (i = 0; i < re->nrepl; i++)
-     {
-         re->nmoves[re->ind[i]][pind[i]] += 1;
-         re->nmoves[pind[i]][re->ind[i]] += 1;
-@@ -1306,10 +1381,14 @@
-      * exchanges. */
-     /* Where each replica ends up after the exchange attempt(s). */
-     /* The order in which multiple exchanges will occur. */
-     gmx_bool bThisReplicaExchanged = FALSE;
- 
-+    /* PLUMED */
-+    if(plumedswitch)plumed_cmd(plumedmain,"GREX prepare",NULL);
-+    /* END PLUMED */
-+
-     if (MASTER(cr))
-     {
-         replica_id  = re->repl;
-         test_for_replica_exchange(fplog, cr->ms, re, enerd, det(state_local->box), step, time);
-         prepare_to_do_exchange(fplog, re->destinations, replica_id, re->nrepl, &maxswap,
-@@ -1355,14 +1434,14 @@
-                 exchange_partner = re->order[replica_id][j];
- 
-                 if (exchange_partner != replica_id)
-                 {
-                     /* Exchange the global states between the master nodes */
--                    if (debug)
--                    {
--                        fprintf(debug, "Exchanging %d with %d\n", replica_id, exchange_partner);
--                    }
-+                    //if (debug)
-+                    //{
-+                        fprintf(fplog, "Exchanging %d with %d\n", replica_id, exchange_partner);
-+                    //}
-                     exchange_state(cr->ms, exchange_partner, state);
-                 }
-             }
-             /* For temperature-type replica exchange, we need to scale
-              * the velocities. */
-EOF_EOF

patches/gromacs-4.6.3.diff/src/kernel/CMakeLists.txt

+#
+# This file is part of the GROMACS molecular simulation package.
+#
+# Copyright (c) 2012,2013, by the GROMACS development team, led by
+# David van der Spoel, Berk Hess, 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.
+#
+
+include(${CMAKE_SOURCE_DIR}/Plumed.cmake)
+
+set(GMXPREPROCESS_SOURCES 
+    add_par.c       
+    calc_verletbuf.c
+    compute_io.c    
+    convparm.c      
+    gen_ad.c        
+    gen_vsite.c     
+    genhydro.c   
+    gpp_atomtype.c  
+    gpp_bond_atomtype.c     
+    h_db.c          
+    hackblock.c             
+    hizzie.c        
+    nm2type.c
+    pdb2top.c       
+    pgutil.c        
+    readir.c        
+    readpull.c      
+    readadress.c      
+    readrot.c
+    resall.c        
+    sorting.c       
+    specbond.c      
+    ter_db.c        
+    tomorse.c       
+    topdirs.c       
+    topexcl.c       
+    topio.c         
+    toppush.c       
+    topshake.c      
+    toputil.c       
+    tpbcmp.c        
+    vsite_parm.c    
+    fflibutil.c
+    xlate.c)
+
+set(MDRUN_SOURCES 
+    gctio.c    ionize.c runner.c
+    do_gct.c     repl_ex.c  xutils.c pme_loadbal.c
+    md.c         mdrun.c    genalg.c membed.c)
+
+add_library(gmxpreprocess ${GMXPREPROCESS_SOURCES})
+target_link_libraries(gmxpreprocess md)
+set_target_properties(gmxpreprocess PROPERTIES OUTPUT_NAME "gmxpreprocess${GMX_LIBS_SUFFIX}" SOVERSION ${SOVERSION} INSTALL_NAME_DIR "${LIB_INSTALL_DIR}"
+    COMPILE_FLAGS "${OpenMP_C_FLAGS}")
+
+
+if(GMX_GPU)
+    include_directories(${CMAKE_SOURCE_DIR}/src/gmxlib/gpu_utils)
+endif()
+
+if(GMX_OPENMM)
+    # Even though the OpenMM build has "moved to contrib", many things
+    # have be be done from within the scope of the CMakeLists.txt that
+    # builds its mdrun, and that is here
+    list(APPEND CMAKE_MODULE_PATH ${CMAKE_SOURCE_DIR}/src/contrib)
+    find_package(OpenMM)
+    include_directories(${CMAKE_CURRENT_SOURCE_DIR})
+    include(${CMAKE_SOURCE_DIR}/src/contrib/BuildMdrunOpenMM.cmake)
+endif(GMX_OPENMM)
+
+if(GMX_GPU OR GMX_FORCE_CXX)
+    set_source_files_properties(main.c PROPERTIES LANGUAGE CXX)
+    if ("${CMAKE_CXX_COMPILER_ID}" STREQUAL "Clang")
+        set_source_files_properties(main.c PROPERTIES COMPILE_FLAGS "-x c++")
+    endif()
+endif()
+
+if(GMX_FAHCORE)
+  add_library(fahcore ${MDRUN_SOURCES})
+else(GMX_FAHCORE)
+
+set(GMX_KERNEL_PROGRAMS
+    grompp tpbconv pdb2gmx g_protonate gmxdump g_x2top gmxcheck)
+if (NOT GMX_NO_QUOTES)
+  set(GMX_KERNEL_PROGRAMS ${GMX_KERNEL_PROGRAMS} g_luck)
+endif (NOT GMX_NO_QUOTES)
+
+
+foreach(PROGRAM ${GMX_KERNEL_PROGRAMS})
+    add_executable(${PROGRAM} ${PROGRAM}.c main.c)
+    if (NOT ${PROGRAM} STREQUAL "g_luck")
+        gmx_add_man_page(${PROGRAM})
+    endif()
+    target_link_libraries(${PROGRAM} gmxpreprocess md gmx ${OpenMP_LINKER_FLAGS})
+    set_target_properties(${PROGRAM} PROPERTIES OUTPUT_NAME "${PROGRAM}${GMX_BINARY_SUFFIX}")
+endforeach()
+
+add_executable(mdrun ${MDRUN_SOURCES} main.c)
+gmx_add_man_page(mdrun)
+target_link_libraries(mdrun gmxpreprocess md gmx ${OpenMP_LINKER_FLAGS} ${PLUMED_LOAD})
+set_target_properties(mdrun PROPERTIES OUTPUT_NAME "mdrun${GMX_BINARY_SUFFIX}" COMPILE_FLAGS "${OpenMP_C_FLAGS}")
+
+if(GMX_OPENMM)
+    target_link_libraries(mdrun openmm_api_wrapper)
+endif()
+
+# Construct component groups for installation; note that a component may
+# belong to only one group
+foreach(PROGRAM ${GMX_KERNEL_PROGRAMS})
+    set(CPACK_COMPONENT_${PROGRAM}_GROUP tools)
+endforeach()
+set(CPACK_COMPONENT_MDRUN_GROUP mdrun)
+
+foreach(PROGRAM ${GMX_KERNEL_PROGRAMS} mdrun)
+    # Manage CPack component dependencies
+    set(CPACK_COMPONENT_${PROGRAM}_DEPENDS libraries libraries-gmxpreprocess)
+
+    # Create custom install-xxxx target
+    if (BUILD_SHARED_LIBS)
+    # If shared libraries are used, we need to install the libraries in
+    # addition to the mdrun binary.
+       add_custom_target(install-${PROGRAM}
+           COMMAND ${CMAKE_COMMAND} -DCOMPONENT=libraries
+                   -P ${CMAKE_BINARY_DIR}/cmake_install.cmake
+           COMMAND ${CMAKE_COMMAND} -DCOMPONENT=libraries-gmxpreprocess
+                   -P ${CMAKE_BINARY_DIR}/cmake_install.cmake
+           COMMAND ${CMAKE_COMMAND} -DCOMPONENT=${PROGRAM}
+                   -P ${CMAKE_BINARY_DIR}/cmake_install.cmake
+           COMMENT "Installing ${PROGRAM}")
+    else()
+       add_custom_target(install-${PROGRAM}
+           COMMAND ${CMAKE_COMMAND} -DCOMPONENT=${PROGRAM}
+                   -P ${CMAKE_BINARY_DIR}/cmake_install.cmake
+           COMMENT "Installing ${PROGRAM}")
+    endif()
+    add_dependencies(install-${PROGRAM} ${PROGRAM})
+
+    # Finally, trigger installation
+    install(
+      TARGETS ${PROGRAM}
+      COMPONENT ${PROGRAM}
+      DESTINATION ${BIN_INSTALL_DIR}
+      )
+endforeach()
+
+install(TARGETS gmxpreprocess DESTINATION ${LIB_INSTALL_DIR} COMPONENT libraries-gmxpreprocess)
+
+if (INSTALL_CUDART_LIB) #can be set manual by user
+    if (GMX_GPU)
+        foreach(CUDA_LIB ${CUDA_LIBRARIES})
+            string(REGEX MATCH "cudart" IS_CUDART ${CUDA_LIB})
+            if(IS_CUDART) #libcuda should not be installed
+                #install also name-links (linker uses those)
+                file(GLOB CUDA_LIBS ${CUDA_LIB}*)
+                install(FILES ${CUDA_LIBS} DESTINATION
+                    ${LIB_INSTALL_DIR} COMPONENT libraries)
+            endif()
+        endforeach()
+    else()
+        message(WARNING "INSTALL_CUDART_LIB only makes sense with GMX_GPU")
+    endif()
+endif ()
+endif(GMX_FAHCORE)
+
+configure_file(${CMAKE_CURRENT_SOURCE_DIR}/libgmxpreprocess.pc.cmakein ${CMAKE_CURRENT_BINARY_DIR}/libgmxpreprocess.pc @ONLY)
+install(FILES ${CMAKE_CURRENT_BINARY_DIR}/libgmxpreprocess.pc
+        DESTINATION ${LIB_INSTALL_DIR}/pkgconfig
+        RENAME "libgmxpreprocess${GMX_LIBS_SUFFIX}.pc"
+        COMPONENT development)

patches/gromacs-4.6.3.diff/src/kernel/CMakeLists.txt.preplumed

+#
+# This file is part of the GROMACS molecular simulation package.
+#
+# Copyright (c) 2012,2013, by the GROMACS development team, led by
+# David van der Spoel, Berk Hess, 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(GMXPREPROCESS_SOURCES 
+    add_par.c       
+    calc_verletbuf.c
+    compute_io.c    
+    convparm.c      
+    gen_ad.c        
+    gen_vsite.c     
+    genhydro.c   
+    gpp_atomtype.c  
+    gpp_bond_atomtype.c     
+    h_db.c          
+    hackblock.c             
+    hizzie.c        
+    nm2type.c
+    pdb2top.c       
+    pgutil.c        
+    readir.c        
+    readpull.c      
+    readadress.c      
+    readrot.c
+    resall.c        
+    sorting.c       
+    specbond.c      
+    ter_db.c        
+    tomorse.c       
+    topdirs.c       
+    topexcl.c       
+    topio.c         
+    toppush.c       
+    topshake.c      
+    toputil.c       
+    tpbcmp.c        
+    vsite_parm.c    
+    fflibutil.c
+    xlate.c)
+
+set(MDRUN_SOURCES 
+    gctio.c    ionize.c runner.c
+    do_gct.c     repl_ex.c  xutils.c pme_loadbal.c
+    md.c         mdrun.c    genalg.c membed.c)
+
+add_library(gmxpreprocess ${GMXPREPROCESS_SOURCES})
+target_link_libraries(gmxpreprocess md)
+set_target_properties(gmxpreprocess PROPERTIES OUTPUT_NAME "gmxpreprocess${GMX_LIBS_SUFFIX}" SOVERSION ${SOVERSION} INSTALL_NAME_DIR "${LIB_INSTALL_DIR}"
+    COMPILE_FLAGS "${OpenMP_C_FLAGS}")
+
+
+if(GMX_GPU)
+    include_directories(${CMAKE_SOURCE_DIR}/src/gmxlib/gpu_utils)
+endif()
+
+if(GMX_OPENMM)
+    # Even though the OpenMM build has "moved to contrib", many things
+    # have be be done from within the scope of the CMakeLists.txt that
+    # builds its mdrun, and that is here
+    list(APPEND CMAKE_MODULE_PATH ${CMAKE_SOURCE_DIR}/src/contrib)
+    find_package(OpenMM)
+    include_directories(${CMAKE_CURRENT_SOURCE_DIR})
+    include(${CMAKE_SOURCE_DIR}/src/contrib/BuildMdrunOpenMM.cmake)
+endif(GMX_OPENMM)
+
+if(GMX_GPU OR GMX_FORCE_CXX)
+    set_source_files_properties(main.c PROPERTIES LANGUAGE CXX)
+    if ("${CMAKE_CXX_COMPILER_ID}" STREQUAL "Clang")
+        set_source_files_properties(main.c PROPERTIES COMPILE_FLAGS "-x c++")
+    endif()
+endif()
+
+if(GMX_FAHCORE)
+  add_library(fahcore ${MDRUN_SOURCES})
+else(GMX_FAHCORE)
+
+set(GMX_KERNEL_PROGRAMS
+    grompp tpbconv pdb2gmx g_protonate gmxdump g_x2top gmxcheck)
+if (NOT GMX_NO_QUOTES)
+  set(GMX_KERNEL_PROGRAMS ${GMX_KERNEL_PROGRAMS} g_luck)
+endif (NOT GMX_NO_QUOTES)
+
+
+foreach(PROGRAM ${GMX_KERNEL_PROGRAMS})
+    add_executable(${PROGRAM} ${PROGRAM}.c main.c)
+    if (NOT ${PROGRAM} STREQUAL "g_luck")
+        gmx_add_man_page(${PROGRAM})
+    endif()
+    target_link_libraries(${PROGRAM} gmxpreprocess md gmx ${OpenMP_LINKER_FLAGS})
+    set_target_properties(${PROGRAM} PROPERTIES OUTPUT_NAME "${PROGRAM}${GMX_BINARY_SUFFIX}")
+endforeach()
+
+add_executable(mdrun ${MDRUN_SOURCES} main.c)
+gmx_add_man_page(mdrun)
+target_link_libraries(mdrun gmxpreprocess md gmx ${OpenMP_LINKER_FLAGS})
+set_target_properties(mdrun PROPERTIES OUTPUT_NAME "mdrun${GMX_BINARY_SUFFIX}" COMPILE_FLAGS "${OpenMP_C_FLAGS}")
+
+if(GMX_OPENMM)
+    target_link_libraries(mdrun openmm_api_wrapper)
+endif()
+
+# Construct component groups for installation; note that a component may
+# belong to only one group
+foreach(PROGRAM ${GMX_KERNEL_PROGRAMS})
+    set(CPACK_COMPONENT_${PROGRAM}_GROUP tools)
+endforeach()
+set(CPACK_COMPONENT_MDRUN_GROUP mdrun)
+
+foreach(PROGRAM ${GMX_KERNEL_PROGRAMS} mdrun)
+    # Manage CPack component dependencies
+    set(CPACK_COMPONENT_${PROGRAM}_DEPENDS libraries libraries-gmxpreprocess)
+
+    # Create custom install-xxxx target
+    if (BUILD_SHARED_LIBS)
+    # If shared libraries are used, we need to install the libraries in
+    # addition to the mdrun binary.
+       add_custom_target(install-${PROGRAM}
+           COMMAND ${CMAKE_COMMAND} -DCOMPONENT=libraries
+                   -P ${CMAKE_BINARY_DIR}/cmake_install.cmake
+           COMMAND ${CMAKE_COMMAND} -DCOMPONENT=libraries-gmxpreprocess
+                   -P ${CMAKE_BINARY_DIR}/cmake_install.cmake
+           COMMAND ${CMAKE_COMMAND} -DCOMPONENT=${PROGRAM}
+                   -P ${CMAKE_BINARY_DIR}/cmake_install.cmake
+           COMMENT "Installing ${PROGRAM}")
+    else()
+       add_custom_target(install-${PROGRAM}
+           COMMAND ${CMAKE_COMMAND} -DCOMPONENT=${PROGRAM}
+                   -P ${CMAKE_BINARY_DIR}/cmake_install.cmake
+           COMMENT "Installing ${PROGRAM}")
+    endif()
+    add_dependencies(install-${PROGRAM} ${PROGRAM})
+
+    # Finally, trigger installation
+    install(
+      TARGETS ${PROGRAM}
+      COMPONENT ${PROGRAM}
+      DESTINATION ${BIN_INSTALL_DIR}
+      )
+endforeach()
+
+install(TARGETS gmxpreprocess DESTINATION ${LIB_INSTALL_DIR} COMPONENT libraries-gmxpreprocess)
+
+if (INSTALL_CUDART_LIB) #can be set manual by user
+    if (GMX_GPU)
+        foreach(CUDA_LIB ${CUDA_LIBRARIES})
+            string(REGEX MATCH "cudart" IS_CUDART ${CUDA_LIB})
+            if(IS_CUDART) #libcuda should not be installed
+                #install also name-links (linker uses those)
+                file(GLOB CUDA_LIBS ${CUDA_LIB}*)
+                install(FILES ${CUDA_LIBS} DESTINATION
+                    ${LIB_INSTALL_DIR} COMPONENT libraries)
+            endif()
+        endforeach()
+    else()
+        message(WARNING "INSTALL_CUDART_LIB only makes sense with GMX_GPU")
+    endif()
+endif ()
+endif(GMX_FAHCORE)
+
+configure_file(${CMAKE_CURRENT_SOURCE_DIR}/libgmxpreprocess.pc.cmakein ${CMAKE_CURRENT_BINARY_DIR}/libgmxpreprocess.pc @ONLY)
+install(FILES ${CMAKE_CURRENT_BINARY_DIR}/libgmxpreprocess.pc
+        DESTINATION ${LIB_INSTALL_DIR}/pkgconfig
+        RENAME "libgmxpreprocess${GMX_LIBS_SUFFIX}.pc"
+        COMPONENT development)