GROMACS

When g_msd is applied to a system with xy periodicity, it stalls, as it continually tries to subtract a zero box vector.

I've added some files to reproduce the error (note that this is a 4.5.5 tpr), with command gmx_msd -s md3.tpr -f md3.xtc. Any group selection will lead to the error.

A proposed change (in 4.6 code) is as follows:

diff --git a/src/tools/gmx_msd.c b/src/tools/gmx_msd.c
index a529b1f..47fb33c 100644
--- a/src/tools/gmx_msd.c
+++ b/src/tools/gmx_msd.c
@ -400,11 +400,15 @ static void prep_data(gmx_bool bMol,int gnx,atom_id index[],

for(m=DIM-1; m>=0; m--) 
         {
+            if (hbox[m] == 0)
+            {
+                continue;
+            }
             while(xcur[ind][m]-xprev[ind][m] <= hbox[m])
                 rvec_inc(xcur[ind],box[m]);
             while(xcur[ind][m]-xprev[ind][m] >  hbox[m])
                 rvec_dec(xcur[ind],box[m]);
        }      
+        }
     }
 }