isdb tutorial: nopbc

[makedoc]

user-doc/tutorials/others/isdb-1.txt

@@ -62,29 +62,29 @@ In order to have a converged sampling for this reference ensemble calculation it
 
 \plumedfile
 # CVs, Psi9, Phi1 are not defined
-psi1: TORSION ATOMS=@psi-1
-psi2: TORSION ATOMS=@psi-2
-psi3: TORSION ATOMS=@psi-3
-psi4: TORSION ATOMS=@psi-4
-psi5: TORSION ATOMS=@psi-5
-psi6: TORSION ATOMS=@psi-6
-psi7: TORSION ATOMS=@psi-7
-psi8: TORSION ATOMS=@psi-8
-
-phi2: TORSION ATOMS=@phi-2
-phi3: TORSION ATOMS=@phi-3
-phi4: TORSION ATOMS=@phi-4
-phi5: TORSION ATOMS=@phi-5
-phi6: TORSION ATOMS=@phi-6
-phi7: TORSION ATOMS=@phi-7
-phi8: TORSION ATOMS=@phi-8
-phi9: TORSION ATOMS=@phi-9
+psi1: TORSION ATOMS=@psi-1 NOPBC
+psi2: TORSION ATOMS=@psi-2 NOPBC
+psi3: TORSION ATOMS=@psi-3 NOPBC
+psi4: TORSION ATOMS=@psi-4 NOPBC
+psi5: TORSION ATOMS=@psi-5 NOPBC
+psi6: TORSION ATOMS=@psi-6 NOPBC
+psi7: TORSION ATOMS=@psi-7 NOPBC
+psi8: TORSION ATOMS=@psi-8 NOPBC
+
+phi2: TORSION ATOMS=@phi-2 NOPBC
+phi3: TORSION ATOMS=@phi-3 NOPBC
+phi4: TORSION ATOMS=@phi-4 NOPBC
+phi5: TORSION ATOMS=@phi-5 NOPBC
+phi6: TORSION ATOMS=@phi-6 NOPBC
+phi7: TORSION ATOMS=@phi-7 NOPBC
+phi8: TORSION ATOMS=@phi-8 NOPBC
+phi9: TORSION ATOMS=@phi-9 NOPBC
 
 ahc:  ALPHARMSD RESIDUES=all TYPE=OPTIMAL LESS_THAN={RATIONAL R_0=0.12}
 
 # Bulky Trp residue dihedral
-dihtrp_cacb: TORSION ATOMS=67,47,49,52
-dihtrp_cbcg: TORSION ATOMS=47,49,52,53
+dihtrp_cacb: TORSION ATOMS=67,47,49,52 NOPBC
+dihtrp_cbcg: TORSION ATOMS=47,49,52,53 NOPBC
 
 protein-ca: GROUP NDX_FILE=index.ndx NDX_GROUP=C-alpha
 gyr: GYRATION TYPE=RADIUS ATOMS=protein-ca NOPBC
@@ -133,6 +133,7 @@ RDC ...
     ADDCOUPLINGS
     GYROM=-72.5388
     SCALE=0.0001
+    NOPBC
     ATOMS1=18,19 COUPLING1=-5.4
     ATOMS2=25,26 COUPLING2=-1.26
     ATOMS3=35,36 COUPLING3=-5.22
@@ -149,6 +150,7 @@ RDC ...
     ADDCOUPLINGS
     GYROM=179.9319
     SCALE=0.0001
+    NOPBC
     ATOMS1=5,6 COUPLING1=12.95
     ATOMS2=27,28 COUPLING2=11.5
     ATOMS3=37,38 COUPLING3=21.42
@@ -163,6 +165,7 @@ RDC ...
 JCOUPLING ...
     ADDCOUPLINGS
     TYPE=HAN
+    NOPBC
     ATOMS1=@psi-2 COUPLING1=-0.49
     ATOMS2=@psi-4 COUPLING2=-0.54
     ATOMS3=@psi-5 COUPLING3=-0.53
@@ -175,6 +178,7 @@ JCOUPLING ...
 JCOUPLING ...
     ADDCOUPLINGS
     TYPE=HAHN
+    NOPBC
     ATOMS1=@phi-2 COUPLING1=6.05
     ATOMS2=@phi-3 COUPLING2=5.95
     ATOMS3=@phi-4 COUPLING3=6.44
@@ -189,6 +193,7 @@ JCOUPLING ...
 JCOUPLING ...
     ADDCOUPLINGS
     TYPE=CCG
+    NOPBC
     ATOMS1=67,47,49,52 COUPLING1=1.59
     LABEL=jccg
 ... JCOUPLING
@@ -197,12 +202,13 @@ JCOUPLING ...
 JCOUPLING ...
     ADDCOUPLINGS
     TYPE=NCG
+    NOPBC
     ATOMS1=47,49,52,53 COUPLING1=1.21
     LABEL=jncg
 ... JCOUPLING
  
 # Chemical shifts
-cs: CS2BACKBONE ATOMS=1-111 NRES=9 DATA=data TEMPLATE=egaawaass.pdb
+cs: CS2BACKBONE ATOMS=1-111 NRES=9 DATA=data TEMPLATE=egaawaass.pdb NOPBC
 
 # metainference entries