From d690f0dba70949852312265c03c8f61b2bebe498 Mon Sep 17 00:00:00 2001
From: carlocamilloni <carlo.camilloni@gmail.com>
Date: Mon, 22 Jul 2019 00:28:21 +0200
Subject: [PATCH] tutorial-2: more
---
user-doc/tutorials/aa-lugano-2.txt | 34 +++++++++++++++++++++++++++--
user-doc/tutorials/lugano-2/wham.py | 6 ++---
2 files changed, 35 insertions(+), 5 deletions(-)
diff --git a/user-doc/tutorials/aa-lugano-2.txt b/user-doc/tutorials/aa-lugano-2.txt
index e27574fad..23b9b9076 100644
--- a/user-doc/tutorials/aa-lugano-2.txt
+++ b/user-doc/tutorials/aa-lugano-2.txt
@@ -305,7 +305,7 @@ restraint-phi: RESTRAINT ARG=phi KAPPA=250.0 AT=$AT
PRINT STRIDE=20 ARG=phi,psi,restraint-phi.bias FILE=COLVAR$AT
EOF
-gmx mdrun -plumed plumed.dat -nsteps 100000 -x traj$AT.xtc -nb cpu
+gmx mdrun -plumed plumed.dat -nsteps 100000 -x traj$AT.xtc -c cout$AT.gro -nb cpu
done
\endverbatim
@@ -379,7 +379,37 @@ python do_fes.py allphi-w.dat 1 -3.1415 3.1415 50 2.49 fes.dat
\endverbatim
the resulting profile will be disappointing, error estimate and convergence will be discussed in the following tutorials,
-but clearly simulations are too short.
+but clearly simulations are too short. A more advanced approach would be to use the configurations obtained from the former
+simulations to generate multiple replicas and then perform the US again for longer time and possible in parallel. The syntax
+is presented in the following but the exercise is possible only if plumed is compiled with mpi
+
+\section lugano-2-ex-5 Exercise 5: WHAM Umbrella Sampling in parallel (optional)
+
+Here we use the "replica" syntax of plumed to write a single plumed input file for all the windows:
+
+\plumedfile
+# vim:ft=plumed
+MOLINFO STRUCTURE=diala.pdb
+phi: TORSION ATOMS=@phi-2
+psi: TORSION ATOMS=@psi-2
+#
+# Impose an umbrella potential on CV 1
+# with a spring constant of 250 kjoule/mol
+# at fixed points along phi
+#
+restraint-phi: RESTRAINT ...
+ ARG=chi KAPPA=250.0
+ AT=@replicas:{
+ -3.00 -2.75 -2.50 -2.25
+ -2.00 -1.75 -1.50 -1.25
+ -1.00 -0.75 -0.50 -0.25
+ 0.00 0.25 0.50 0.75
+ 1.00 1.25 1.50 1.75
+ 2.00 2.25 2.50 2.75 3.00
+} ...
+# monitor the two variables and the bias potential from the restraint
+PRINT STRIDE=20 ARG=phi,psi,restraint-phi.bias FILE=COLVAR
+\endplumedfile
WHAM is also natively implemented in PLUMED but requires the use of parallel processes with mpi.
diff --git a/user-doc/tutorials/lugano-2/wham.py b/user-doc/tutorials/lugano-2/wham.py
index dad15a1d2..2d666e3d0 100644
--- a/user-doc/tutorials/lugano-2/wham.py
+++ b/user-doc/tutorials/lugano-2/wham.py
@@ -65,9 +65,9 @@ for lines in open(FILENAME_, "r").readlines():
if(riga[0]=="#!"): continue
# read bias values
# umbrella-sampling typical format
- if(len(riga) == NBIAS_):
- i0 = 0
- i1 = NBIAS_
+ if(len(riga) == NBIAS_+1):
+ i0 = 1
+ i1 = NBIAS_+1
# bias exchange typical format
elif(len(riga) == 2*NBIAS_+1):
i0 = NBIAS_+1
--
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