Namd-Qm/Mm Tutorial: Unix/Macosx Version
Namd-Qm/Mm Tutorial: Unix/Macosx Version
Namd-Qm/Mm Tutorial: Unix/Macosx Version
NAMD-QM/MM
TUTORIAL
Unix/MacOSX Version
December 2017
Contents
1 Basics of QM/MM 6
1.1 What is Needed . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
1.2 Preparing Your System . . . . . . . . . . . . . . . . . . . . . . . 6
1.3 Preparing Your QM/MM Simulation . . . . . . . . . . . . . . . . 9
2 Advanced 16
3 Acknowledgment 17
CONTENTS 3
Introduction
This tutorial provides a first introduction to NAMD-QM/MM interface and its
basic capabilities. It can also be used as an introduction for the non-expert
QM/MM user.
The tutorial assumes that you already have a working knowledge of VMD
and that NAMD 2.12 or later has been installed correctly on your computer.
For installation instructions, please refer to the NAMD User’s Guide. For the
accompanying VMD tutorial go to
http://www.ks.uiuc.edu/Training/Tutorials/
System Requirements
The QM/MM interface of NAMD/VMD is available for MacOS X and Unix.
• Mac
Operating System: Mac OS X 10.4.7 or later
Memory: 1 GB RAM
Processor: Intel Core 2 Duo 2.0 Ghz CPU (or comparable)
Graphics card: NVIDIA GeForce 320M, or comparable
• Linux
Operating System: Any reliable Linux distribution released within the
last three years.
Memory: 1 GB RAM
Processor: Intel Core 2 Duo 2.0 Ghz CPU (or comparable)
Graphics card: NVIDIA GeForce 320M, or comparable
Required Programs
For more details check http://www.ks.uiuc.edu/Research/qmmm/
Installation Guide
Both NAMD and VMD are distributed pre-compiled. In both cases instala-
tion can be performed in less than a minute. More information available at
http://www.ks.uiuc.edu/Development/
• NAMD: A NAMD binary distribution need only be untarred or unzipped
and can be run directly in the resulting directory. When building from
source code, “make release” will generate a self-contained directory and
.tar.gz or .zip archive that can be moved to the desired installation loca-
tion. Windows and CUDA builds include Tcl .dll and CUDA .so files that
must be in the dynamic library path.
• VMD: To install the pre-compiled MacOS X bundle version of VMD,
open the VMD disk image and drag the VMD application into an appro-
priate directory. Once the VMD application has been placed appropriately
it should be ready for immediate use as no other installation steps are re-
quired.
To install the pre-compiled Unix version of VMD, then only three steps
remain to be done after you uncompress and untar the distribution.
Edit the configure script. If necessary, change the following values:
$install bin dir
This is the location of the startup script ’vmd’. It should be located in
the path of users interested in running VMD.
$install library dir
This is the location of all other VMD files. This includes the binary and
helper scripts. It should not be in the path.
Next generate the Makefile based on these configuration variables. This
is done by running ./configure .
After configuration is complete, cd to the src directory and type make
install. This will put the code in the two directories listed above. After
this, you just type vmd to begin, provided that vmd is in your path.
• ORCA: Instructions available at:
https://orcaforum.cec.mpg.de/
• MOPAC: Instructions available at:
http://openmopac.net/manual/Installing MOPAC.html
Getting Started
• If you have downloaded this tutorial at home, you will also need to down-
load the appropriate files, unzip them, place them in a directory of your
choosing, and then navigate to that directory.
1 BASICS OF QM/MM 6
1 Basics of QM/MM
In this section you will learn how to use the NAMD-QM/MM interface to set
up basic molecular dynamics (MD) simulations that use classical and quantum
mechanical calculations. You will learn about typical input and output files, and
basic options available to set up your simulation.
• a Protein Data Bank (pdb) file which stores atomic coordinates and/or
velocities for the system. Pdb files may be generated by hand, but they are
also available via the Internet for many proteins at http://www.pdb.org.
• a Protein Structure File (psf) which stores structural information of the
protein, such as various types of bonding interactions.
• a configuration file, in which the user specifies all the options that NAMD
should adopt in running a simulation. The configuration file tells NAMD
how the QM/MM simulation is to be run and how the QM code is to be
executed.
• a “QM”-PDB file which indicates how atoms are partitioned in different
QM regions. QM-PDB files may be generated by hand or by using VMD’s
QwikMD interface, as will be demonstrated in this tutorial.
1 Open VMD and then open QwikMD by clicking Extensions -> Simulation
-> QwikMD menu item in the VMD main window.
1 BASICS OF QM/MM 7
2 Type 4b9f in the navigation bar and click “Load”. This will automatically
download the PDB file form the PDB databank.
You should see the window populated with information from the downloaded
structure (Figure 1a) and the structure will be displayed in VMD’s main window
(Figure 2). We will only use one of the protein chains displayed in the X-ray
structure, so our system will only contain one protein chain and one Calcium-
binding site.
5 Still on the “Structure Manipulation”, select the residue 153 and click on
the “Rename” button. Now click on the “Res NAME” field of the line
and select “Calcium” from the drop-down list. Now click on the “Apply”
button (Figure 3b).
Now that we have the desired protein and ion complex, we need to prepare
the system for an MD simulation, where we will equilibrate the structure before
beginning a QM/MM simulations. The protein-ion complex will be placed in a
water box with counter ions.
1 BASICS OF QM/MM 9
7 In the main QwikMD window, click on the “Advanced run” tab, and then
on the “MD” tab. Then check the box for “Minimal Box”. and select a
12 Åbuffer of solvent molecules around our protein (Figure 4a).
8 Finally, in the “Protocol” section, select the “MD” line and click the “-”
(minus) button to remove this simulations step. Prepare your simulation
under the “Simulation Setup” section and run it. The results will be used
to initialize the QM/MM simulation.
Figure 4: a) QwikMD main window indicating the selection of the “MD” simula-
tion step. b) Highlight for the “Prepare” option with all simulation parameters
set.
In this tutorial, you should load only the data from the equilibration trajec-
tory, and mark that only the last step of the simulation should be loaded. We
are using the last step form the classical equilibration step to select our QM
region and initiate the QM/MM simulation.
2 In the “QM Options” section, make sure the “QM Software” indicates
MOPAC. If it does not, select it form the drop-down menu (Figure 5b).
3 In the “QM Regions” section, click the “+” (plus) button to define a
new QM region in your system. A new line should appear in this section
(Figure 5b).
4 Click on the “n Atoms” column (see Figure 5b) to open the “QM Region
Selection” window (Figure 7a) .
1 BASICS OF QM/MM 11
5 In the “QM Region Selection” window (Figure 7b), change the radius
for solvent within the QM region to 5 Å. Now scroll down the residue
list in the same window until you find the Calcium residue (Res ID: 153;
Res NAME: CAL) and click on that line. The calcium ion and two water
molecules should be selected. Click “Apply” so QwikMD can process your
selection.
The new selection will be displayed by QwikMD with 7 atoms (the calcium
ion and two water molecules) and the total charge shown on the window will be
updated to +2. Since this is outside the ±1 range, a representation similar to
1 BASICS OF QM/MM 13
Figure 8 will be created, indicating charged residues near the QM region (red
for negatively charged and blue for positively charged).
6 Click on the transparent red residues and note the charge of the QM region
changing to reflect the new selection.
NOTE: Every time you add or remove a residue from the QM region selec-
tion, QwikMD will update the selection of water molecules to reflect the new
QM region selection.
7 In the “QM Region Selection” window, click on the Clear Selection button
(if you closed the window, just go to QwikMD’s main window, go to “QM
Regions”, and click on the QM region line under the “n Atoms” column).
1 BASICS OF QM/MM 14
Figure 8: VMD main window showing the selected QM region in solid colors,
and nearby charged residues in transparent red representation for negatively
charged and transparent blue for positively charged.
9 Place the cursor in the Atom Selection text field and type the following
selection: same residue as (within 5 of (resname CAL)).
The parenthesis are not necessary in this selection, but helps us parse the
statement. This selection is made using VMD’s atomselect language, which
allows easy and flexible selection of regions within your system using logical
statements and direct access to properties of atoms and residues. To understand
this selection, we will read it starting from its inner most statement: First, we
select every residue with name CAL, which only occurs once in this particular
system, and is the Calcium ion. We then extend the selection to include every
1 BASICS OF QM/MM 15
atom within 5 Åof the residue, and then expand it again to include all atoms of
residues that were partially included in the 5 Åradius around the Calcium ion
(Figure 9). Once again, assuming you loaded the pre-ran MD results provided
with this tutorial, a total of 148 atoms will be selected by this “Atom Selection”
statement.
We can now proceed to prepare the simulation by clearing the path shown in
the Simulation Setup section, and clicking on “Prepare”. You will give a path
to the location where all input and configuration files will be saved, and when
2 ADVANCED 16
asked which starting step you would like to use, select Equilibration.
NOTE: Reduced output files are provided with this tutorial, since a 500
thousand step simulation accumulates too much information for it to be feasi-
ble to download and analyze quickly.
2 Advanced
Speeding-up every-step I/O
If you are using a Linux distribution, it is possible to create a folder for tem-
porary files mounted directly on RAM, usually by creating a folder under
/dev/shm. You can change where NAMD stores temporary files from QM ex-
ecutions by clicking on a protocol, such as the QMMM-Min line, under the
Protocol section, and clicking on the Edit button. This will show you the com-
plete NAMD configuration file, where you can change any detail for the selected
simulation step. The path given to the qmBaseDir keyword is the one used to
run QM calculations, and can be substituted by the folder you created. Changes
must be made to each protocol individually.
creation commands:
• mol representation CPK 1.1 0.3 8.0 6.0 1.5
3 Acknowledgment
The developement of NAMD and the tutorials are funded by the National In-
stitute of Health (P41- RR005969 - Resource for Macromolecular Modeling and
Bioinformatics). Proper citation is a primary way in which we demonstrate the
value of our software to the scientic community, and is essential to continued
NIH funding for NAMD. The authors request that all published work which
utilizes NAMD/VMD include the primary NAMD/VMD citations: