From f2c395067cff71d7d369b083e19c44f200b10e72 Mon Sep 17 00:00:00 2001
From: carlocamilloni <carlo.camilloni@gmail.com>
Date: Sun, 13 Aug 2017 17:50:15 +0200
Subject: [PATCH] isdb tutorial: nopbc [makedoc]
---
user-doc/tutorials/others/isdb-1.txt | 46 ++++++++++++++++------------
1 file changed, 26 insertions(+), 20 deletions(-)
diff --git a/user-doc/tutorials/others/isdb-1.txt b/user-doc/tutorials/others/isdb-1.txt
index 138cacf43..98b5fad80 100644
--- a/user-doc/tutorials/others/isdb-1.txt
+++ b/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
--
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