diff --git a/Configuration.cpp b/Configuration.cpp
index b4fbcc9061a7c1a921be9278a0678f5519f4d42f..5a818d26cd4ada1c4a4cb6e330c46a6775fe13bb 100644
--- a/Configuration.cpp
+++ b/Configuration.cpp
@@ -1059,7 +1059,7 @@ void Configuration::readBonds() {
 		}
 		
 		// If we don't have enough room in our bond array, we need to expand it.
-		if (numBonds >= capacity) {
+		if (numBonds+1 >= capacity) { // "numBonds+1" because we are adding two bonds to array
 			// Temporary pointer to the old array
 			Bond* temp = bonds;	
 
@@ -1087,6 +1087,11 @@ void Configuration::readBonds() {
 			continue;
 		}*/
 
+		if (ind1 < 0 || ind1 >= num || ind2 < 0 || ind2 >=num) {
+			printf("ERROR: Bond file line '%s' includes invalid index\n", line);
+			exit(1);
+		}
+
 		Bond* b = new Bond(op, ind1, ind2, file_name);
 		bonds[numBonds++] = *b;
 		b = new Bond(op, ind2, ind1, file_name);
diff --git a/notes.org b/notes.org
index c748a8de6b25b53a27957057508260da87e19409..a98f8d4263ef5c9b5b173f21da9ba5c8261a16f6 100644
--- a/notes.org
+++ b/notes.org
@@ -12,6 +12,7 @@
 
 
 * TODO eventually
+** enable flag to disable physics-checking assertions in kernels (also write these assertions)
 ** split computation into multiple regions
 *** simulate regions, also in overlap
 **** atoms at edge of overlap can have DoF frozen