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Molecular Modeling and Visualization
Molecular Modeling and Visualization
This guide helps you to get started with molecular dynamics and computational chemistry packages installed in HPC, and use appropriate visualization tools to analyze and visualize the outputs.
Important Notes
Important Notes
Refer to Evolution of Quantum Theory
Refer to Evolution of Quantum Chemistry
Running Job in HPC
Running Job in HPC
You can copy the sample files from /usr/local/doc/MolecularModeling and change directory to specific Software directory.
cp -r /usr/local/doc/MolecularModeling .
cd gaussian # for Gaussian
Gaussian
Gaussian
Interactive Job:
In the hpc Linux terminal, type the following to request a compute node with x11-forwarding option. For better visualization experience, refer to HPC GUI Visual Access.
srun --x11 --mem=4gb --pty bash
Refer to HPC Guide to Gaussian for details.
Example: Toluene - methylbenzene [4]
Load the Gaussian Module and run GaussView
module load gaussian
gview &
In the GaussView GUI, build a Tolune molecule following the instruction at [4].
New -> create Molecule Group
View -> Builder (from where you are going to add element and fragments)
Click on the new window to get the fragment imported to the file
Find the buttons to select, deselect, delete fragments, crate bond etc.
Improve the Geometry by clicking the clean up button which will use a MM calculation to optimize the geometry quickly.
Save the structure as .COM file; you can save it as pdb (Protein Data Bank) format as well
Alternatively, you can open the Gaussian input or setup file "toluene.com" from /usr/local/doc/MolecularModeling/gaussian which produces the molecule as in Fig. 1.
Fig. 1 Toluene molecule in GaussView
View the toluene.com file
cat tolune.com
output:
%nprocshared=4
%mem=16MW
%chk=toluene.chk
# opt=calcfc freq=raman b3lyp/6-31g(d) geom=connectivity
tolune
0 1
C -2.30021599 -0.39956803 0.00000000
...
H 1.68892795 -0.07145942 0.49472818
1 2 1.5 6 1.5 7 1.0
...
The brief description is given below but for details, refer to Gaussian Tutorial [5]. You can also check Calculate->Gaussian Calculation Setup ...
Job Type: Opt+Freq
Compute Raman: Yes
Calculate Force Constants: Once
Method:
Method: Ground State; DFT; Default Spin; B3LYP
Basis Set: 6-31G d
Charge:0
Spin:Singlet
Title: tolune
Link0:
Memory Limit: Specify -> 16 MW
Chkpoint File: Specify -> tolune.chk
Shared Processors: Specify -> 4
The first line in the zmatrix section that describes the location of each atom in the molecule specifies:
Atom 1, connected with atom 2, atom 6, and atom 7 with bond length 1.5, 1.5 and 1.0 respectively.
Batch job:
You can now submit the Gaussian job as a batch job submission. Find the job file "toluene.job" in the gaussian directory and submit
sbatch toluene.job
You will get the output file "toluene.log:
Entering Gaussian System, Link 0=g09
Input=toluene.com
Output=toluene.log
Initial command:
/usr/local/gaussian/09/g09/l1.exe /scratch/pbsjobs/gaussian/Gau-7576.inp -scrdir=/scratch/pbsjobs/gaussian/
Entering Link 1 = /usr/local/gaussian/09/g09/l1.exe PID= 7577.
Copyright (c) 1988,1990,1992,1993,1995,1998,2003,2009, Gaussian, Inc.
All Rights Reserved.
...
Will use up to 4 processors via shared memory.
%mem=16MW
%chk=toluene.chk
--------------------------------------------------------
# opt=calcfc freq=raman b3lyp/6-31g(d) geom=connectivity
--------------------------------------------------------
1/10=4,14=-1,18=20,19=15,26=3,38=1,57=2/1,3;
6/7=2,8=2,9=2,10=2,19=2,28=1/1;
99/9=1/99;
------
tolune
------
Symbolic Z-matrix:
Charge = 0 Multiplicity = 1
C -2.30022 -0.39957 0.
...
Predicted change in Energy=-3.941680D-09
Optimization completed on the basis of negligible forces.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.3955 -DE/DX = 0.0 !
! R2 R(1,6) 1.3959 -DE/DX = 0.0 !
! R3 R(1,7) 1.0871 -DE/DX = 0.0 !
...
Job cpu time: 0 days 0 hours 6 minutes 49.0 seconds.
File lengths (MBytes): RWF= 34 Int= 0 D2E= 0 Chk= 2 Scr= 1
Normal termination of Gaussian 09 at Fri Jul 21 13:30:41 2017.
Analyze and Visualize:
To view this output in GaussView:
Open the GaussView if it has been closed:
gview &
File -> Open and browse to the output/log file selecting File Type: Gaussian Output Files.
Click on Result -> Vibrations and in the Vibration window click "Start Animation". You will notice the vibration.
Now, click Spectrum to see the IR spectrum as showed in Fig. 2.
Fig. 2: IR Spectrum for Toluene
Visit and ParaView
Visit and ParaView
The molecule can be visualized in Scientific visualization tools like Visit and ParaView for higher resolution. Please refer to HPC Visit Guide and HPC ParaView Guide for details.
Visit:
Make sure that you have saved toulene.com also in .pdb format
Get the compute node referring to "Interactive Visual Session" section above.
Load the module and open the GUI
module load visit
visit &
In the GUI:
File -> Open and browse to toluen.pdb and ok
Add-> Molecule-> backbone -> Draw (you will see the Toluene molecule as showed:
Fig. 3: Toluene molecule in Visit.
Want to change plot attributes? PlottsAtt-> Molecule ...
Controls->Annotations ->uncheck showgrid, show triad, and show...
VMD
VMD
Please refer to HPC VMD Guide and VMD Protein Simulation tutorial [6].
Load the module and open the GUI
module load visit
vmd &
In the GUI:
File -> New Molecule ->Browse -> toluene.pdb
Graphic -> Representation->Coloring Method->Element->Drawing Method (CPK) i.e. ball and stick; Also, set bond resolution and sphere resolution as desired.
Mouse-Label->Atoms->click on the atoms for labels
File->render->Tachyon
Click on start rendering; you will see the data file (vmdscene.dat) and the image file (vmdscene.dat.tga)
In the vmdscene.dat file, the resolution is set to 669 x 630 "Resolution 669 630" ; You can change it and re-render it
OR
Exentisons->Tk Console->command:
loading history file ... 4 events added
Main console display active (Tcl8.5.6 / Tk8.5.6)
(Gaussian) 5 % display resize 1050 800
>Main< (Gaussian) 6 % display vmdscene.dat.tga
Animation (Movie):
Exentions->Visualization->Movie Maker
Select the renderer -> Tachycon
Click on Set working directory where you want the movie file and Name of Movie
Click on Make Movie
VMD with NAMD
VMD with NAMD
Simulation:
load the NAMD module. Refer to HPC NAMD Guide for details.
module load namd
Extensions->Simulations->NAMD Graphical Interface
Check the box next to "Minimization" under time steps -> Run NAMD
You will see NAMD config file "toluene.namd" and "toluene_fixed.pdb"
For details on MD Simulations, visit 1UBQ example [7].
Get tutorial files at http://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-files/1-1-build/
Search for 1UBQ in protein database at http://www.pdb.org and download the pdb file
VASPTools
VASPTools
Please refer to HPC Guide to VASPTools.
References:
[1] Evolution of Quantum Theory
[2] HPC Guide to Molecular Modeling Software
[4] Quantum Chemistry with Gaussian using GaussView
[6] VMD Protein Simulation tutorial
[7] MD Simulations
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