MD Simulations with Gromacs - Revision history

Ballen: /* Procedure */

2019-02-22T03:27:01Z

Procedure

Ballen: /* Procedure */

2019-02-22T03:20:13Z

Procedure

Ballen: /* Procedure */

2019-02-22T03:10:55Z

Procedure

Ballen at 03:10, 22 February 2019

2019-02-22T03:10:20Z

Ballen: /* Set-Up */

2019-02-22T02:46:43Z

Set-Up

Ballen at 02:02, 22 February 2019

2019-02-22T02:02:59Z

Ballen at 02:01, 22 February 2019

2019-02-22T02:01:50Z

Ballen at 19:50, 21 February 2019

2019-02-21T19:50:39Z

Ballen: Created page with "== Overview == This page is intended to serve as a resource for those interested in doing MD Simulations with Gromacs. == Set-Up == The first step is to download the Gro..."

2019-02-21T19:50:12Z

Created page with "== Overview == This page is intended to serve as a resource for those interested in doing MD Simulations with Gromacs. == Set-Up == The first step is to download the Gro..."

New page

== Overview ==

This page is intended to serve as a resource for those interested in doing MD Simulations with Gromacs.

== Set-Up ==

The first step is to download the Gromacs software. This can be done by navigating to the Gromacs Documentation page, found [http://manual.gromacs.org/documentation/ here] and then clicking on Download under the most recent version. This one is currently 2019.1.

The next step is to click on the link next to "as http".

The installation guide can be found [http://manual.gromacs.org/documentation/current/install-guide/index.html here]. I provide this because this is a process that is operating system specific, so I will focus my Set-Up instructions for those that are working on Mac OS.

Now that you have hopefully downloaded a .tar of the Gromacs software, you will have to "unzip" the tar ball. This can be done by opening a terminal and typing the following:

'tar xfz gromacs-2019.tar'

Note that the "gromacs-2019.tar" should reflect whatever the name of your downloaded file is. Next, you navigate to the directory that you have just created by typing:

'cd Gromacs-2019'

← Older revision		Revision as of 03:27, 22 February 2019
Line 54:		Line 54:

	''gmx pdb2gmx -f KALP-15_princ.pdb -o KALP-15_processed.gro -ignh -ter -water spc''		''gmx pdb2gmx -f KALP-15_princ.pdb -o KALP-15_processed.gro -ignh -ter -water spc''
		+
		+	Next, you should choose the GROMOS96 53A6 parameter set... This is done by typing the number in front of this set. For me, it was 13.
		+
		+	Choose none for both termini. This is done by typing the number in front of the "None" option. For me, this was 2. (twice)
		+
		+	Next, you will have to download the lipid parameter files titled:
		+
		+	*dppc128.pdb - the structure of a 128-lipid DPPC bilayer
		+	*dppc.itp - the moleculetype definition for DPPC
		+	*lipid.itp - Berger lipid parameters
		+
		+	and can be found [http://wcm.ucalgary.ca/tieleman/downloads here!]

← Older revision		Revision as of 03:20, 22 February 2019
Line 42:		Line 42:
	Here is a flowchart depicting the general procedure for running a GROMACS MD Simulation:		Here is a flowchart depicting the general procedure for running a GROMACS MD Simulation:
	[[File:Gromacs scheme.png\|800px\|framed\|center\|A flowchart for a typical GROMACS MD Simulation run of a protein in a box of water. ]]		[[File:Gromacs scheme.png\|800px\|framed\|center\|A flowchart for a typical GROMACS MD Simulation run of a protein in a box of water. ]]
		+
		+	The first thing that we will do to see what GROMACS is capable of is follow a tutorial for KALP-15 in a DPPC bilayer. You can find a series of tutorials [http://www.mdtutorials.com/gmx/ here]!
		+
		+	Step 1: You need to get a .pdf file. You can get that file [http://www.mdtutorials.com/gmx/membrane_protein/Files/KALP-15_princ.pdb here].
		+
		+	Then, navigate to the directory where this is located. It is likely in your Downloads folder, so you can navigate there by typing the following command into the terminal window:
		+
		+	''cd Downloads''
		+
		+	Then type the following into the terminal:
		+
		+	''gmx pdb2gmx -f KALP-15_princ.pdb -o KALP-15_processed.gro -ignh -ter -water spc''

@@ Line 40: / Line 40: @@
 == Procedure ==
+Here is a flowchart depicting the general procedure for running a GROMACS MD Simulation:
 [[File:Gromacs scheme.png|800px|framed|center|A flowchart for a typical GROMACS MD Simulation run of a protein in a box of water. ]]

← Older revision		Revision as of 03:10, 22 February 2019
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	If you get some kind of error (i.e. command not found), then you should go back to the documentation. Otherwise, you are ready to get started!		If you get some kind of error (i.e. command not found), then you should go back to the documentation. Otherwise, you are ready to get started!
		+
		+	== Procedure ==
		+
		+	[[File:Gromacs scheme.png\|800px\|framed\|center\|A flowchart for a typical GROMACS MD Simulation run of a protein in a box of water. ]]

@@ Line 16: / Line 16: @@
       ''tar xfz gromacs-2019.tar''
-Note that the "gromacs-2019.tar" should reflect whatever the name of your downloaded file is. Next, you navigate to the directory that you have just created by typing:
+Note that the "gromacs-2019.tar" should reflect whatever the name of your downloaded file is. At this point, I would like to point out that you will need a compiler called Cmake in order to successfully install Gromacs. I was able to download this using  Homebrew, which may or may not be possible for you. If you do not have homebrew, then you can download Cmake from [https://cmake.org/download/ this webpage!]
       ''cd Gromacs-2019''
@@ Line 26: / Line 30: @@
       ''sudo make install''
       ''source /usr/local/gromacs/bin/GMXRC''

← Older revision		Revision as of 02:02, 22 February 2019
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	Now that you have hopefully downloaded a .tar of the Gromacs software, you will have to "unzip" the tar ball. This can be done by opening a terminal and typing the following:		Now that you have hopefully downloaded a .tar of the Gromacs software, you will have to "unzip" the tar ball. This can be done by opening a terminal and typing the following:

		+	''cd Downloads''
	''tar xfz gromacs-2019.tar''		''tar xfz gromacs-2019.tar''

← Older revision		Revision as of 02:01, 22 February 2019
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	''cd Gromacs-2019''		''cd Gromacs-2019''
		+	''mkdir build''
		+	''cd build''
		+	''cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON''
		+	''make''
		+	''make check''
		+	''sudo make install''
		+	''source /usr/local/gromacs/bin/GMXRC''