diff --git a/.gitignore b/.gitignore
index 7ba099c740265f2e7020ab6776d7948211f64a99..f5834bd729d96cca37aab626a938fd9a9bd128a8 100644
--- a/.gitignore
+++ b/.gitignore
@@ -29,6 +29,7 @@
 .~lock.*
 
 # Autotools
+aclocal.m4
 autom4te.cache
 .deps
 stamp-h1
@@ -37,6 +38,7 @@ config.guess
 config.status
 config.sub
 configure
+libtool
 Makefile
 Makefile.in
 
diff --git a/puremd_rc_1003/PG-PuReMD/src/.gitignore b/puremd_rc_1003/PG-PuReMD/src/.gitignore
new file mode 100644
index 0000000000000000000000000000000000000000..592fe6602ff1ba6214746cf3b5473fa16eeda75e
--- /dev/null
+++ b/puremd_rc_1003/PG-PuReMD/src/.gitignore
@@ -0,0 +1 @@
+pg-puremd
diff --git a/puremd_rc_1003/PuReMD-GPU/src/.gitignore b/puremd_rc_1003/PuReMD-GPU/src/.gitignore
new file mode 100644
index 0000000000000000000000000000000000000000..de9f888cb11c97e4272ba22ecff75abffecb5404
--- /dev/null
+++ b/puremd_rc_1003/PuReMD-GPU/src/.gitignore
@@ -0,0 +1 @@
+puremd-gpu
diff --git a/puremd_rc_1003/PuReMD/src/.gitignore b/puremd_rc_1003/PuReMD/src/.gitignore
new file mode 100644
index 0000000000000000000000000000000000000000..6331f666f79fb6a51ea03d210e966b31af215a78
--- /dev/null
+++ b/puremd_rc_1003/PuReMD/src/.gitignore
@@ -0,0 +1 @@
+puremd
diff --git a/puremd_rc_1003/environ/parallel_control b/puremd_rc_1003/environ/parallel_control
index 57e9fab3c8cfa9a8879a4e5d8971b6e55e929a15..7918661761ad18b812a740498beaf3bbfcaf81a2 100644
--- a/puremd_rc_1003/environ/parallel_control
+++ b/puremd_rc_1003/environ/parallel_control
@@ -1,7 +1,7 @@
 simulation_name	        water.6.112    ! output files will carry this name + their specific ext.
 ensemble_type	 	1	! 0: NVE  1: Berendsen NVT  2: Nose-Hoover NVT(under testing)  3: semi-isotropic NPT  4: isotropic NPT  5: anisotropic NPT (under development)
-nsteps			10    ! number of simulation steps
-dt			0.25 	! time step in fs
+nsteps			100    ! number of simulation steps
+dt			0.10 	! time step in fs
 proc_by_dim             1 1 2   ! distribution of processors by dimensions
 geo_format 		1 	! 0: custom  1: pdb (only if natoms < 100000) 2: ASCII restart 3: binary restart
 
diff --git a/puremd_rc_1003/sPuReMD/src/.gitignore b/puremd_rc_1003/sPuReMD/src/.gitignore
new file mode 100644
index 0000000000000000000000000000000000000000..d47a7ab9231081b36aa8f2290d1173361c1c334f
--- /dev/null
+++ b/puremd_rc_1003/sPuReMD/src/.gitignore
@@ -0,0 +1 @@
+spuremd