diff --git a/tools/replica/reorder_remd_traj.py b/tools/replica/reorder_remd_traj.py
index c8c467ffe0..cef417cd0b 100644
--- a/tools/replica/reorder_remd_traj.py
+++ b/tools/replica/reorder_remd_traj.py
@@ -38,11 +38,11 @@ StringIO (or io if in Python 3.x)
 
 
 
-import os, sys, numpy as np, argparse, time, pickle
+import os, numpy as np, argparse, time, pickle
 from scipy.special import logsumexp
 from mpi4py import MPI
 
-from tqdm import tqdm, trange
+from tqdm import tqdm
 import gzip, bz2
 try:
     # python-2
@@ -78,12 +78,10 @@ def _get_nearest_temp(temps, query_temp):
     """
     
     if isinstance(temps, list): temps = np.array(temps)
-    idx = np.argmin(abs(temps - query_temp))
-    out_temp = temps[idx]
-    return out_temp
+    return temps[np.argmin(np.abs(temps-query_temp))]
 
 
-def readwrite(trajfn, mode = "rb"):
+def readwrite(trajfn, mode):
     """ 
     Helper function for input/output LAMMPS traj files.
     Trajectories may be plain text, .gz or .bz2 compressed.
@@ -96,11 +94,14 @@ def readwrite(trajfn, mode = "rb"):
     """
     
     if trajfn.endswith(".gz"):
-        return gzip.GzipFile(trajfn, mode)
+        of = gzip.open(trajfn, mode)
+        #return gzip.GzipFile(trajfn, mode)
     elif trajfn.endswith(".bz2"):
-        return bz2.BZ2File(trajfn, mode)
+        of = bz2.open(trajfn, mode)
+        #return bz2.BZ2File(trajfn, mode)
     else:
-        return file(trajfn, mode)
+        of = open(trajfn, mode)
+    return of
 
 
 def get_replica_frames(logfn, temps, nswap, writefreq):
@@ -163,7 +164,7 @@ def get_byte_index(rep_inds, byteindfns, intrajfns):
         if os.path.isfile(byteindfns[n]): continue
         
         # extract bytes
-        fobj = readwrite(intrajfns[n]) 
+        fobj = readwrite(intrajfns[n], "rb") 
         byteinds = [ [0,0] ]
         
         # place file pointer at first line
@@ -243,7 +244,7 @@ def write_reordered_traj(temp_inds, byte_inds, outtemps, temps,
     for n in temp_inds:
         # open string-buffer and file
         buf = IOBuffer()
-        of = readwrite(outtrajfns[n], mode = "wb")
+        of = readwrite(outtrajfns[n], "wb")
         
         # get frames
         abs_temp_ind = np.argmin( abs(temps - outtemps[n]) )
@@ -281,7 +282,7 @@ def write_reordered_traj(temp_inds, byte_inds, outtemps, temps,
         
         
 def get_canonical_logw(enefn, frametuple_dict, temps, nprod, writefreq,
-                       kB = 0.001987):
+                       kB):
     """
     Gets configurational log-weights (logw) for each frame and at each temp.
     from the REMD simulation. ONLY WRITTEN FOR THE CANONICAL (NVT) ensemble.
@@ -348,25 +349,25 @@ def get_canonical_logw(enefn, frametuple_dict, temps, nprod, writefreq,
     #3) get reduced energies (*ONLY FOR THE CANONICAL ENSEMBLE*)
     u_kln = np.zeros([ntemps, ntemps, nframes], float)
     for k in range(ntemps):
-        for l in range(ntemps):
-            u_kln[ k, l, 0:nframes_k[k] ] = beta_k[l] * u_kn[k, 0:nframes_k[k]]
-    
+        u_kln[k] = np.outer(beta_k, u_kn[k])
+        
     # run pymbar and extract the free energies
     print("\nRunning pymbar...")
     mbar = pymbar.mbar.MBAR(u_kln, nframes_k, verbose = True)
-    f_k = mbar.f_k
+    f_k = mbar.f_k # (1 x k array)
 
     # calculate the log-weights
     print("\nExtracting log-weights...")
     log_nframes = np.log(nframes)
     logw = dict( (k, np.zeros([ntemps, nframes], float)) for k in range(ntemps) )
-    for l in range(ntemps):
-        # get log-weights to reweight to this temp.
-        for k in range(ntemps):
-            for n in range(nframes):
-                num = -beta_k[k] * u_kn[k,n]
-                denom = f_k - beta_k[k] * u_kn[k,n]
+    # get log-weights to reweight to this temp.
+    for k in range(ntemps):
+        for n in range(nframes):
+            num = -beta_k[k] * u_kn[k,n]
+            denom = f_k - beta_k[k] * u_kn[k,n]
+            for l in range(ntemps):
                 logw[l][k,n] = num - logsumexp(denom) - log_nframes
+            
     return logw
 
 
@@ -515,7 +516,7 @@ if __name__ == "__main__":
     comm.barrier()
     
     # open all replica files for reading
-    infobjs = [readwrite(i) for i in intrajfns]
+    infobjs = [readwrite(i, "rb") for i in intrajfns]
     
     # open all byteindex files
     byte_inds = dict( (i, np.loadtxt(fn)) for i, fn in enumerate(byteindfns) )