From 3798f44b33199a2a1b3d2ccdf37bf2c718da3055 Mon Sep 17 00:00:00 2001
From: Massimiliano Bonomi <massimiliano.bonomi@gmail.com>
Date: Wed, 24 May 2017 11:47:11 +0200
Subject: [PATCH] adding further details to tutorial 6
---
user-doc/tutorials/a-trieste-6.txt | 24 +++++++++++++++++++++---
1 file changed, 21 insertions(+), 3 deletions(-)
diff --git a/user-doc/tutorials/a-trieste-6.txt b/user-doc/tutorials/a-trieste-6.txt
index c3eea6fbd..839f9179c 100644
--- a/user-doc/tutorials/a-trieste-6.txt
+++ b/user-doc/tutorials/a-trieste-6.txt
@@ -85,7 +85,7 @@ chainA: GROUP ATOMS=1,3,5,7,9,10,12,15,17,19,21,23,25,27,29,31,33,34,36,38,41,43
# backbone beads index for chain B
chainB: GROUP ATOMS=226,228,230,232,234,235,238,239,240,245,246,250,252,255,256,257,259,261,264,266,268,271,273,275,278,280,282,285,287,289,291,293,295,298,300,302,304,306,308,309,310,312,314,318,320,324,326,328,330,332,334,336,338,340,342,343,345,346,348,350,352,354,358,360,362,363,368,370,372,374,376,379,381,383,386,388,390,392,394,396,398,400,402,404,406,409,411,414,416,418,420,424,426,428,430,432,434
-coord: COORDINATION GROUPA=chainA GROUPB=chainB NOPBC D_0=1.0
+coord: COORDINATION GROUPA=chainA GROUPB=chainB NOPBC R_0=1.0
\endplumedfile
3) A CV describing the relative orientation of the two chains.
@@ -122,6 +122,7 @@ of a single molecule of urea.
using `VMD`.
The users are expected to:
+- characterize the conformational ensemble of cmyc by calculating free-energies as a function of different CVs.
- calculate the fraction of bound and unbound molecules of urea by defining suitable CVs to measure
the position of urea relative to cmyc.
- find the cmyc aminoacids that bind urea the most and the least.
@@ -138,12 +139,31 @@ the conformational landscape of cmyc:
2) the content of alpha (\ref ALPHARMSD) and beta (\ref ANTIBETARMSD) secondary structure
+The fraction of bound and unbound molecules of urea can be computed after evaluating the minimum distance
+among all the distances between heavy atoms of cmyc and urea, as follows:
+
+\plumedfile
+# cmyc heavy atoms
+cmyc: GROUP ATOMS=5,6,7,9,11,14,15,17,19,22,24,26,27,28,30,32,34,38,41,45,46,47,49,51,54,56,60,64,65,66,68,70,73,75,76,77,79,81,83,87,91,92,93,95,97,100,103,104,105,108,109,110,112,114,118,119,120,122,124,127,130,131,132,133,134,135,137,139,142,145,146,147,148,149,150,152,154,157,160,161,162,165,166,167,169,171,174,177,180,183,187,188
+
+# urea heavy atoms
+urea: GROUP ATOMS=192,193,194,197
+
+# minimum distance cmyc-urea
+mindist: DISTANCES GROUPA=cmyc GROUPB=urea MIN={BETA=500.}
+\endplumedfile
+
+For estimating the cmyc aminoacid that bind the most and the least urea, we leave the users the choice of the best
+strategy.
+
For the calculation of ensemble averages of experimental CVs, we suggest to use:
1) 3J scalar couplings (\ref JCOUPLING)
2) the FRET intensity between termini (\ref FRET)
+and we encourage the users to look at the examples provided in the manual for the exact syntax.
+
\section trieste-6-ex-3 Exercize 3: Protein G folding simulations
GB1 is a small protein domain with a simple beta-alpha-beta fold. It is a well studied protein that folds on the millisecond time scale.
Here we use a structure based potential and well-tempered metadynamics to study the free energy of folding and unfolding.
@@ -186,5 +206,3 @@ In summary, in this tutorial you should have learned how to use PLUMED to:
link: @subpage trieste-6
description: This tutorial explains how to use PLUMED to run metadynamics simulations
-
-additional-files: trieste-6
--
GitLab