(0) Place WP2.tar.gz into a directory and
$ tar -zxvf WP2.tar.gz
The command will generate a directory WP2 with subdirectory
/examples
This exercises will require running a full version of the MOSAICS software
and its potential and topology libraries. If the required software installed
in your computer, just make 3 local soft links to the executable, potential
and topology libraries into the WP2/examples library. To do this
$ cd WP2/examples
$ ln -s $(YOUR-PATH-TO-MOSAICS-EXECUTABLE)/mosaics.x mosaics.x
$ ln -s $(YOUR-PATH-TO-MOSAICS-TOPOLOGY--DATABASE)/top_database top_database
$ ln -s $(YOUR-PATH-TO-MOSAICS-POTENTIAL-DATABASE)/pot_database pot_database
Note (14/03/2016): Konrad Krawczyk installed MOSAICS and the potential and
topology libraries on all DTC computers. Therefore, you may create the
following soft links to complete your installation.
$ ln -s /home/bio/MOSAICS/PyMosaics/MosaicsInstallation/mosaics.x mosaics.x
$ ln -s /home/bio/MOSAICS/PyMosaics/MosaicsInstallation/lib/top_database/ top_database
$ ln -s /home/bio/MOSAICS/PyMosaics/MosaicsInstallation/lib/pot_database/ pot_database
----------------------------------------------------------------------------
If you don't have either the code or the libraries already installed in your
computer, we provide it on the Computational Biology Practical Website following
the link at www.cs.ox.ac.uk/mosaics. By clicking the links
and you can download MOSAICS.tar.gz and TOPPOT.tar.gz files. Next
extract these files in the same directory you extracted your files for the
work packages (WPs). Then
$ tar -zxvf TOPPOT.tar.gz
$ tar -zxvf MOSAICS.tar.gz
# compile MOSAICS following the
# instructions at www.cs.ox.ac.uk/mosaics
$ cd WP2/examples
$ ln -s ../../MOSAICS/version.3.9.1_bgq/examples/mosaics.x mosaics.x
$ ln -s ../../TOPPOT/top_database/ top_database
$ ln -s ../../TOPPOT/pot_database/ pot_database
---------------------------------------------------------------------------
In the following I assume that you have three local links in WP2/examples,
e.g if you installed your own version your local library has this structure
drwxr-xr-x 2x3b_dna
drwxr-xr-x 6b_rna
lrwxr-xr-x mosaics.x -> ../../MOSAICS/version.3.9.1_bgq/examples/mosaics.x
lrwxr-xr-x pot_database -> ../../TOPPOT/pot_database/
lrwxr-xr-x top_database -> ../../TOPPOT/top_database/
(1) In WP2/examples there are two systems an rna and a dna fragment (.pdb files)
each containing 6 nucleotides. The systems has the same size, yet they have
a very different topology; the rna is a 6 base unstructured loop whereas the
dna is composed of three base pairs. You can visualize the .pdb files using
Pymol or VMD software packages available in your computer.
Next, we suggest you try running mosaics.x using the following
syntax:
$ cd 6b_rna
$ ../mosaics.x mcmc.input > output
where mcmc.input is your input file, in which you can set the simulation
parameters. Some of the parameters carry function related names but you
can read the description of each simulation parameter in the online manual
following the link on the MOSAICS website www.cs.ox.ac.uk
Every time you run your examples, you are going to generate the following
files:
output : contains detailed information about your system and simulation
results such as acceptance rate
.pos.pdb : contains your trajectory in .pdb format
.pos_out.pdb : your last conformation in your trajectory in .pdb format
.pot_energy : potential energy as a function of steps
.inter_energy : intermolecular energy vs MC iteration
.tors_pos : the trajectory in torsion angle space
sim_param.out : contains all the simulation parameters you used for this run
the file also lists all simulation parameters you could change
for this MOSAICS version but they will take their indicated
default values unless you set them separately
Before you attempt a new run, you may want to delete all output files with
the script provided
$ ./clean
$ ../mosaics.x mcmc.input > output
or using the one line version
$ ./clean; ../mosaics.x mcmc.input > output
(2) In this exercise we ask you to generate a short, only 10,000 mc step length
MCMC trajectory in both cartesian space and dihedral (torsional) space for
both systems. For this you only have to change the \prop_type{} option in the
mcmc.input file.
\prop_type{cart} using Cartesian degrees of freedom
\prop_type{tors} using torsional degrees of freedom
Please run and save these short trajectories for both systems and compare
the results focusing on the trajectory files (.pos.pdb), which you can visualize
using either Pymol or VMD Software packages available in your desktop. Compare
the overall acceptance rates, which are printed at the end of your output files.
After you generate these 4 trajectories you may answer the following questions:
How do the trajectories and the overall acceptance rates compare?
Can you qualitatively rank the efficiency of conformational exploration? e.g.
#1 system X using \prop_type{Z} option
#2 system Y using \prop_type{Z} option
..
(*) To give you a hint one of your systems with torsional propagation will produce the
worst acceptance rate
(3) Run and save a further trajectory with the system that produced the worst acceptance
rate with torsional propagation using chain break and closure (JCB, Minary et al. 2010)
based torsional propagation. This option can be turned on if you change the first line
in your initial .pdb file from "# CBLC > ..." to "CBLC > ...".
This option (Constant Bond Length Closure) lets you changing the conformation of
each nucleotide independently that may result in breaking bonds along the atomic
chain connecting adjacent nucleotides. Next, all these chain breaks are restored
using a linear complexity chain closure algorithm (JCB, 2010).
Has the acceptance rate improved?
(4) Given that now we can model systems as a collection of independent nucleotides
we are able to generate correlated motions by moving groups of nucleotides together
in addition to more refined moves that are responsible for the relative orientation
and position of each individual nucleotide within the group. For example, one typical
choice for the dna system would be to move a basepair collectively.
After turning on the option learned in (3) for both dna and rna systems, please activate
the "region" option in you mcmc.input file by changing
region_database_file{region/region.data}
to
\region_database_file{region/region.data}
The region.data file lets you specify how the individual elements of your region
are grouped and the relative magnitude of collective and non collective motions.
In addition, it lets you control rotational and translation type of motions
separately therefore gives you a great deal of flexibility that you can explore in
this exercise. Before you do so, please browse the content of "2x3b_dna/region/README"
file that explains you the meaning of each line used in region.data
!!!! Note that the regional or "natural" moves are superimposed on top of the
individual moves of nucleotides we had in (3). Therefore I suggest to turn off non
regional moves so that the control over degrees of freedom is completely handled
in the region file. Please set the following parameters in your mcmc.input file:
\prop_tors_sig{0.0}
\prop_trans_sig{0.0}
\prop_rot_sig{0.0}