********>bugfix 15
Author: Daniel R. Roe
Date: 02/09/2009

Programs: sander 

Description: Adds ability to write formatted REMD trajectories by adding 
             replica temperature variable to trajectory file. Modifies
             bintraj.f

Usage: Save this file in your $AMBERHOME directory and then apply this patch
       file to your amber 10 distribution as follows:

cd $AMBERHOME
patch -p0 -N -r patch_rejects < bugfix

------------------------------------------------------------------------------

--- src/sander/bintraj.f	2008-07-16 10:22:58.000000000 -0400
+++ src/sander/bintraj.f	2008-09-02 17:14:47.000000000 -0400
@@ -10,7 +10,7 @@
 
    integer :: crd_ncid, vel_ncid, oldMode, cmode, atomCnt
    integer :: FrameDimID,SpatialDimID, AtomDimID, LabelDimID, Cell_spatialDimID, Cell_angularDimID
-   integer :: CoordVarID, Cell_lengthVarID, Cell_angleVarID, SpatialVarID, VelocVarID
+   integer :: CoordVarID, Cell_lengthVarID, Cell_angleVarID, SpatialVarID, VelocVarID, TempVarID
    integer :: Cell_spatialVarID, Cell_angularVarID, crd_TimeVarID, vel_TimeVarID
    integer :: crd_frame, vel_frame
 
@@ -23,6 +23,9 @@
 
 #ifdef BINTRAJ
    use netcdf
+#  ifdef MPI
+      use remd, only: rem
+#  endif 
 
    implicit none
 
@@ -52,6 +55,15 @@
          call checkerror(nf90_put_att(crd_ncid, CoordVarID, "units", &
                "angstrom"), "define coordinates units")
       end if
+#  ifdef MPI
+      ! For remd define replica temperature
+      if (rem>0) then
+         call checkerror(nf90_def_var(crd_ncid,"temp0",nf90_double, &
+               (/ FrameDimID /), TempVarID), "define temp0")
+         call checkerror(nf90_put_att(crd_ncid, TempVarID, "units", &
+               "kelvin"), "define temp0 units")
+      endif
+#  endif
       ! Define unit cell data for periodic simulations
       if (ntb > 0 ) then
          if (crd_file_exists) then
@@ -163,6 +175,9 @@
 subroutine write_binary_traj(r,istart,n,unit)
    use netcdf
    use nblist, only: a,b,c,alpha,beta,gamma
+#  ifdef MPI
+      use remd, only: rem,mytargettemp
+#  endif 
    
    implicit none
 #  include "files.h"
@@ -181,6 +196,14 @@
             call checkerror(nf90_put_var(crd_ncid,CoordVarID, r(istart:n), &
                   start = (/ 1, 1, crd_frame /),count = (/ 3, (n-istart+1)/3, 1 /)), &
                   'write atom coords')
+#  ifdef MPI
+            ! If this is a replica run write temp0
+            if (rem>0) then
+               call checkerror(nf90_put_var(crd_ncid,TempVarID,mytargettemp, &
+                     start = (/ crd_frame /) ), &
+                     'write replica mytargettemp')
+            endif
+#  endif
          end if
       case (MDVEL_UNIT)
          call checkerror(nf90_put_var(vel_ncid,VelocVarID, r(istart:n), &