Allow for "computational electrophysiology" simulations (CompEl)

[alexxy/gromacs.git] / src / gromacs / gmxana / gmx_make_ndx.c

diff --git a/src/gromacs/gmxana/gmx_make_ndx.c b/src/gromacs/gmxana/gmx_make_ndx.c
index a5bb67e4a27ae1baea42d13c2c90e747a334ac91..d2a58ab14c2a067027097428511eda70f3e6b4cd 100644 (file)
--- a/src/gromacs/gmxana/gmx_make_ndx.c
+++ b/src/gromacs/gmxana/gmx_make_ndx.c
@@ -1511,14 +1511,20 @@ int gmx_make_ndx(int argc, char *argv[])
         "When a run input file is supplied you can also select on atom type.",
         "You can use NOT, AND and OR, you can split groups",
         "into chains, residues or atoms. You can delete and rename groups.[PAR]",
-        "The atom numbering in the editor and the index file starts at 1."
+        "The atom numbering in the editor and the index file starts at 1.[PAR]",
+        "The [TT]-twin[tt] switch duplicates all index groups with an offset of",
+        "[TT]-natoms[tt], which is useful for Computational Electrophysiology",
+        "double-layer membrane setups."
     };
 
-    static int      natoms   = 0;
-    static gmx_bool bVerbose = FALSE;
-    t_pargs         pa[]     = {
+    static int      natoms     = 0;
+    static gmx_bool bVerbose   = FALSE;
+    static gmx_bool bDuplicate = FALSE;
+    t_pargs         pa[]       = {
         { "-natoms",  FALSE, etINT, {&natoms},
           "set number of atoms (default: read from coordinate or index file)" },
+        { "-twin",     FALSE, etBOOL, {&bDuplicate},
+          "Duplicate all index groups with an offset of -natoms" },
         { "-verbose", FALSE, etBOOL, {&bVerbose},
           "HIDDENVerbose output" }
     };
@@ -1622,7 +1628,7 @@ int gmx_make_ndx(int argc, char *argv[])
 
     edit_index(natoms, atoms, x, block, &gnames, bVerbose);
 
-    write_index(ndxoutfile, block, gnames);
+    write_index(ndxoutfile, block, gnames, bDuplicate, natoms);
 
     return 0;
 }