diff -bur NAMD_2.11_Source/arch/Linux-x86_64.cuda NAMD_2.11_Source-edited/arch/Linux-x86_64.cuda
--- NAMD_2.11_Source/arch/Linux-x86_64.cuda	2015-08-07 14:34:14.000000000 -0600
+++ NAMD_2.11_Source-edited/arch/Linux-x86_64.cuda	2017-03-30 15:40:33.282263643 -0600
@@ -1,12 +1,15 @@
 
-CUDADIR=/usr/local/encap/cuda-6.0
-CUDAINCL=-I$(CUDADIR)/include
-CUDALIB=-L$(CUDADIR)/lib64 -lcudart_static -lrt
-CUDASODIR=$(CUDADIR)/lib64
+CUDADIR=
+CUDAINCL=-I/usr/include
+CUBDIR=.rootdir/cub
+CUBINCL=-I$(CUBDIR)
+CUDALIB=-L/usr/lib -lcufft_static -lculibos -lcudart_static -lrt
+CUDASODIR=/usr/lib
 LIBCUDARTSO=
-CUDAFLAGS=-DNAMD_CUDA
+CUDAFLAGS=-D_FORCE_INLINES -DNAMD_CUDA
 CUDAOBJS=$(CUDAOBJSRAW)
 CUDA=$(CUDAFLAGS) -I. $(CUDAINCL)
-CUDACC=$(CUDADIR)/bin/nvcc -O3 --maxrregcount 32 $(CUDAGENCODE) -Xcompiler "-m64" $(CUDA)
-CUDAGENCODE=-gencode arch=compute_20,code=sm_20 -gencode arch=compute_20,code=compute_20 -gencode arch=compute_35,code=sm_35 -gencode arch=compute_35,code=compute_35 -gencode arch=compute_50,code=sm_50 -gencode arch=compute_50,code=compute_50
+CUDACC=/usr/bin/nvcc -O3 --maxrregcount 48 $(CUDAGENCODE) -Xcompiler "-m64" $(CUDA)
+CUDADLINKOPTS=-gencode arch=compute_30,code=sm_30 -gencode arch=compute_35,code=sm_35 -gencode arch=compute_50,code=sm_50 -gencode arch=compute_60,code=sm_60 -gencode arch=compute_60,code=compute_60
+CUDAGENCODE=-gencode arch=compute_30,code=sm_30 -gencode arch=compute_35,code=sm_35 -gencode arch=compute_37,code=sm_37 -gencode arch=compute_50,code=sm_50 -gencode arch=compute_52,code=sm_52 -gencode arch=compute_60,code=sm_60 -gencode arch=compute_61,code=sm_61 -gencode arch=compute_61,code=compute_61
 
diff -bur NAMD_2.11_Source/arch/Linux-x86_64.fftw3 NAMD_2.11_Source-edited/arch/Linux-x86_64.fftw3
--- NAMD_2.11_Source/arch/Linux-x86_64.fftw3	2011-07-12 12:23:09.000000000 -0600
+++ NAMD_2.11_Source-edited/arch/Linux-x86_64.fftw3	2016-07-19 10:22:49.544924149 -0600
@@ -1,7 +1,7 @@
 
 FFTDIR=$(HOME)/fftw3
-FFTINCL=-I$(FFTDIR)/include
-FFTLIB=-L$(FFTDIR)/lib -lfftw3f
+FFTINCL=-I/usr/include
+FFTLIB=-L/usr/lib -lfftw3f
 FFTFLAGS=-DNAMD_FFTW -DNAMD_FFTW_3
 FFT=$(FFTINCL) $(FFTFLAGS)
 
diff -bur NAMD_2.11_Source/arch/Linux-x86_64.tcl NAMD_2.11_Source-edited/arch/Linux-x86_64.tcl
--- NAMD_2.11_Source/arch/Linux-x86_64.tcl	2011-06-17 14:38:43.000000000 -0600
+++ NAMD_2.11_Source-edited/arch/Linux-x86_64.tcl	2016-07-19 10:28:02.458475804 -0600
@@ -1,9 +1,9 @@
 
 #TCLDIR=/Projects/namd2/tcl/tcl8.5.9-linux-x86_64
 TCLDIR=/Projects/namd2/tcl/tcl8.5.9-linux-x86_64-threaded
-TCLINCL=-I$(TCLDIR)/include
+TCLINCL=-I/usr/include/tcl
 #TCLLIB=-L$(TCLDIR)/lib -ltcl8.5 -ldl
-TCLLIB=-L$(TCLDIR)/lib -ltcl8.5 -ldl -lpthread
+TCLLIB=-L/usr/lib -ltcl8.6 -ldl -lpthread
 TCLFLAGS=-DNAMD_TCL
 TCL=$(TCLINCL) $(TCLFLAGS)
 
Only in NAMD_2.11_Source-edited/: charm-6.7.0
Only in NAMD_2.11_Source-edited/: Linux-x86_64-g++
diff -bur NAMD_2.11_Source/Makefile NAMD_2.11_Source-edited/Makefile
--- NAMD_2.11_Source/Makefile	2015-12-20 15:30:25.000000000 -0700
+++ NAMD_2.11_Source-edited/Makefile	2016-09-15 16:45:01.050425871 -0600
@@ -361,6 +361,8 @@
 
 PLUGINLIB = $(PLUGINOBJS)
 
+include .rootdir/Plumed.inc
+
 CUDAOBJSRAW = \
 	$(DSTDIR)/ComputePmeCUDAKernel.o \
 	$(DSTDIR)/ComputeNonbondedCUDAKernel.o
@@ -452,6 +454,7 @@
 	$(DPMELIB) \
 	$(FMMLIB) \
 	$(TCLLIB) \
+        $(PLUMED_LOAD) \
 	$(FFTLIB) \
 	$(PLUGINLIB) \
 	$(SBLIB) \
Only in NAMD_2.11_Source-edited/: Makefile.preplumed
Only in NAMD_2.11_Source-edited/: Plumed.cmake
Only in NAMD_2.11_Source-edited/: Plumed.h
Only in NAMD_2.11_Source-edited/: Plumed.inc
diff -bur NAMD_2.11_Source/src/ComputeMgr.C NAMD_2.11_Source-edited/src/ComputeMgr.C
--- NAMD_2.11_Source/src/ComputeMgr.C	2015-09-25 14:07:00.000000000 -0600
+++ NAMD_2.11_Source-edited/src/ComputeMgr.C	2016-09-15 16:45:01.062425930 -0600
@@ -87,8 +87,131 @@
 #include "GlobalMasterSymmetry.h"
 #include "GlobalMasterEasy.h"
 #include "GlobalMasterMisc.h"
+// PLUMED
+#include "../Plumed.h"
+// END PLUMED
 #include "GlobalMasterFreeEnergy.h"
 #include "GlobalMasterColvars.h"
+class GlobalMasterPlumed:
+  public  GlobalMasterEasy,
+  private PLMD::Plumed
+{
+  std::vector<int> index;
+  std::vector<double> positions;
+  std::vector<double> forces;
+  std::vector<double> masses;
+  std::vector<double> charges;
+  double box[3][3];
+  SimParameters *spar;
+public:
+  GlobalMasterPlumed():
+    GlobalMasterEasy("plumedScript")
+  {
+    easy_init(config);
+  }
+  void easy_init(const char* config)
+  {
+    int realPrecision=sizeof(double);
+    cmd("setRealPrecision",&realPrecision);
+    spar=Node::Object()->simParameters;
+
+    double energyUnits=4.184;
+    double lengthUnits=0.1;
+    double timeUnits=0.001;
+    cmd("setMDEnergyUnits",&energyUnits);
+    cmd("setMDLengthUnits",&lengthUnits);
+    cmd("setMDTimeUnits",&timeUnits);
+
+    cmd("setPlumedDat",spar->plumedFilename);
+
+    int natoms=Node::Object()->molecule->numAtoms;
+    cmd("setNatoms",&natoms);
+
+    cmd("setMDEngine","namd");
+
+    cmd("setLog",stdout);
+
+    double dt=spar->dt;
+    cmd("setTimestep",&dt);
+    cmd("setNoVirial");
+    cmd("init");
+
+    int s=step+1;
+    cmd("setStep",&s);
+    share();
+
+  }
+
+  void share(){
+    int* p;
+    int n;
+    bool redo=false;
+    cmd("prepareDependencies");
+    cmd("createFullList",&n);
+    cmd("getFullList",&p);
+    if(index.size()!=n)redo=true;
+    if(!redo) for(int i=0;i<n;i++) if(index[i]!=p[i]) { redo=true; break;};
+    if(redo){
+      index.resize(n);
+      masses.resize(n);
+      modifyRequestedAtoms().resize(0);
+      for(int i=0;i<n;i++){
+        requestAtom(p[i]);
+        masses[i]=getMass(p[i]);  
+        index[i]=p[i];
+      };
+      positions.resize(3*n);
+      forces.resize(3*n);
+      charges.resize(n);
+      
+      cmd("setAtomsNlocal",&n);
+      cmd("setAtomsGatindex",&index[0]);
+    }
+    cmd("clearFullList");
+  }
+
+  void easy_calc(){
+
+    for(int i=0;i<index.size();i++){
+      Vector coord;
+      getPosition(index[i],coord);
+      positions[3*i+0]=coord.x;
+      positions[3*i+1]=coord.y;
+      positions[3*i+2]=coord.z;
+      masses[i]=Node::Object()->molecule->atommass(index[i]);
+      charges[i]=Node::Object()->molecule->atomcharge(index[i]);
+    };
+
+    if(spar->lattice.volume()>0.0){
+      for(int i=0;i<3;i++) box[0][i]=spar->lattice.a()[i];
+      for(int i=0;i<3;i++) box[1][i]=spar->lattice.b()[i];
+      for(int i=0;i<3;i++) box[2][i]=spar->lattice.c()[i];
+      cmd("setBox",&box[0][0]);
+    } 
+
+    for(int i=0;i<forces.size();i++) forces[i]=0.0;
+
+    cmd("setMasses",&masses[0]); cmd("setCharges",&charges[0]);
+    cmd("setPositions",&positions[0]);
+    cmd("setForces",&forces[0]);
+
+    cmd("shareData");
+    cmd("performCalc");
+
+    for(int i=0;i<index.size();i++){
+      Vector f;
+      f.x=forces[3*i+0];
+      f.y=forces[3*i+1];
+      f.z=forces[3*i+2];
+      int j=addForce(index[i],f);
+    };
+
+    int s=step+1;
+    cmd("setStep",&s);
+    share();
+ 
+  }
+};
 
 #include "ComputeNonbondedMICKernel.h"
 
@@ -862,6 +985,11 @@
             masterServerObject->addClient(new GlobalMasterTMD());
         if (simParams->miscForcesOn)
             masterServerObject->addClient(new GlobalMasterMisc());
+     // PLUMED
+        if (simParams->plumedOn){
+          masterServerObject->addClient(new GlobalMasterPlumed());
+        }
+     // END PLUMED
         if ( simParams->freeEnergyOn )
             masterServerObject->addClient(new GlobalMasterFreeEnergy());
 		if ( simParams->colvarsOn )
Only in NAMD_2.11_Source-edited/src: ComputeMgr.C.preplumed
diff -bur NAMD_2.11_Source/src/SimParameters.C NAMD_2.11_Source-edited/src/SimParameters.C
--- NAMD_2.11_Source/src/SimParameters.C	2015-12-08 08:41:37.000000000 -0700
+++ NAMD_2.11_Source-edited/src/SimParameters.C	2016-09-15 16:45:01.078426010 -0600
@@ -1500,6 +1500,13 @@
    opts.optionalB("main", "GBISSer", "Use GB implicit solvent?",
       &GBISserOn, FALSE);
 
+
+     // PLUMED
+     //// plumed
+     opts.optionalB("main", "plumed", "Is PLUMED active?",&plumedOn,FALSE);
+     opts.require("plumed", "plumedfile","PLUMED script",PARSE_STRING);
+     // END PLUMED
+
    opts.optional("GBIS", "solventDielectric",
       "Solvent Dielectric", &solvent_dielectric, 78.5);
    opts.optional("GBIS", "intrinsicRadiusOffset",
@@ -4600,7 +4607,7 @@
    // Global forces configuration
 
    globalForcesOn = ( tclForcesOn || freeEnergyOn || miscForcesOn ||
-                      (IMDon && ! IMDignore) || SMDOn || TMDOn || colvarsOn || symmetryOn );
+                      (IMDon && ! IMDignore) || SMDOn || TMDOn || colvarsOn || symmetryOn || plumedOn );
 
 
    if (tclForcesOn)
@@ -4685,6 +4692,21 @@
      iout << endi;
    }
 
+   // PLUMED
+   if (plumedOn)
+   {
+       iout << iINFO << "PLUMED ACTIVE\n";
+
+       current = config->find("plumedfile");
+       iout << iINFO << "PLUMED CONFIG FILE   "<< current->data << "\n" << endi;
+       strcpy(plumedFilename,current->data);
+
+       ifstream plumedFile(current->data);
+       if ( ! plumedFile ) NAMD_die("Error reading PLUMED config file.\n");
+
+   }
+   // END PLUMED
+
    if (IMDon)
    {
      iout << iINFO << "INTERACTIVE MD ACTIVE\n";
Only in NAMD_2.11_Source-edited/src: SimParameters.C.preplumed
diff -bur NAMD_2.11_Source/src/SimParameters.h NAMD_2.11_Source-edited/src/SimParameters.h
--- NAMD_2.11_Source/src/SimParameters.h	2015-09-04 16:20:03.000000000 -0600
+++ NAMD_2.11_Source-edited/src/SimParameters.h	2016-09-15 16:45:01.090426069 -0600
@@ -468,6 +468,9 @@
 	Bool miscForcesOn;		//  Using misc forces?
 	Bool colvarsOn;         //  Using the colvars module?
 
+        Bool plumedOn;                  //  Using Plumed?
+        char plumedFilename[1024];      // Plumed filename
+
 	Bool fixedAtomsOn;		//  Are there fixed atoms?
 	Bool fixedAtomsForces;		//  Calculate forces anyway?
 	Bool fixedAtomsForceOutput; // Output fixed forces?
Only in NAMD_2.11_Source-edited/src: SimParameters.h.preplumed