Gromacs/C3/Solvate-and-Grompp-Commands/English - Revision history

Snehalathak at 06:20, 14 December 2021

2021-12-14T06:20:33Z

2021-12-14T06:04:09Z

2021-12-09T08:25:59Z

2021-12-09T08:00:36Z

2021-12-09T07:58:25Z

2021-12-09T01:47:03Z

2021-12-08T17:21:05Z

2021-12-08T17:14:34Z

2021-11-10T09:26:39Z

2021-11-10T09:04:23Z

@@ Line 391: / Line 391: @@
 || The '''genion''' command adds ions to the system.
-'''pname''' is for positive ion and NA stand for sodium ion.
+'''pname''' is for positive ion and NA stands for sodium ion.
 '''nname''' is for negative ion, which is chloride ions here.

@@ Line 88: / Line 88: @@
 Show the files.
-|| Search for file with '''.gro''' extension and notice few files in it.
+|| Search for file with '''gro''' extension and notice few files in it.
 Water and '''methanol''' solvent types are available in the downloaded files.

@@ Line 339: / Line 339: @@
 |-
 || Scroll up the file.
-| " | Scroll up and notice the file and the many details added to the structure file.
+| " | Scroll up and notice the many details added to the structure file.
 |-
@@ Line 349: / Line 349: @@
 || Open the file manager.
-First find the charge on the system from the topology file.
+Find the charge on the system from the topology file.
 |-

@@ Line 34: / Line 34: @@
 || To record this tutorial, I am using
-* '''Ubuntu Linux''' v20.04 OS
+* '''Ubuntu Linux''' version 20.04 OS
-* '''Gromacs''' v2021.2
+* '''Gromacs''' 2021.2
-* '''Firefox''' web browser v92
+* '''Firefox''' web browser 92
-* '''Gedit''' v3.36
+* '''Gedit''' 3.36
 * '''VMD''' 1.9.3

@@ Line 17: / Line 17: @@
 * Solvent input files with coordinates
 * Add solvent molecules to the system with '''solvate''' command
-* Open the '''solvated.gro''' file in '''VMD'''
+* Open the '''solvated gro''' file in '''VMD'''
 |-

@@ Line 268: / Line 268: @@
 |-
 ||
-|| For this purpose, we will create an '''mdp''' file.
+|| For this purpose, we will create a '''mdp''' file.
 |-
@@ Line 334: / Line 334: @@
 || I will clear the screen for clarity.
 |-
-|| Type,
+|| Type, '''gmx dump -s input1.tpr''' and press '''Enter'''.
-−
 '''gmx dump -s input1.tpr''' and press '''Enter'''.
 | " | Let’s use the '''dump''' command as seen here to make it readable.
@@ Line 349: / Line 347: @@
 |-
 || Open the file manager.
-|| Let’s open the file manager.
+|| Open the file manager.
 First find the charge on the system from the topology file.
@@ Line 400: / Line 398: @@
 |-
 || Press the '''Enter''' key'''.'''
-|| The '''nn 8''' flag can be replaced by '''neutral''' flag to create a neutral system.
+|| The '''nn''' flag can be replaced by '''neutral''' flag to create a neutral system.
 |-

@@ Line 153: / Line 153: @@
 |-
 ||
-|| Let’s command add the water molecules inside the box around '''lysozyme'''.
+|| Let’s add the water molecules inside the box around '''lysozyme'''.
 |-
@@ Line 167: / Line 167: @@
 |-
 || Highlight '''-cp '''.
-|| Here '''-cp''' flag denotes the input file.
+|| Here '''-cp''' flag denotes the input file of the protein structure.
 |-
@@ Line 205: / Line 205: @@
 |-
 || Type, '''vmd solvated.gro''' and press '''Enter'''.
-|| Enter '''vmd''' space '''solvated.pdb''', to open the newly created file in '''VMD'''.
+|| Enter '''vmd''' space '''solvated.gro''', to open the newly created file in '''VMD'''.
 |-
@@ Line 257: / Line 257: @@
 |-
 ||
-|| Next, we will add ions to the system to neutralize the let charge.
+|| Next, we will add ions to the system to neutralize the net charge.
 |-
@@ Line 268: / Line 268: @@
 |-
 ||
-|| For this purpose, we will use an '''mdp''' file.
+|| For this purpose, we will create an '''mdp''' file.
 |-

@@ Line 64: / Line 64: @@
 Show files in the '''firstmd''' working directory.
-|| Open '''File manager''' .
+|| Open the '''File manager''' .
 Copy the necessary input files to the working directory.
@@ Line 94: / Line 94: @@
 |-
 || Cursor on the water solvent files.
-|| Notice files with water solvation in different types.
+|| Notice files, with water solvation in different types.
 |-
@@ Line 143: / Line 143: @@
 |-
 || Show the graphics interface.
-|| '''VMD''' opens with the aligned, centered molecule in the graphics interface.
+|| '''VMD''' opens the aligned, centered molecule in the graphics interface.
 |-

@@ Line 345: / Line 345: @@
 |-
 || Show the '''dump''' file.
-|| Let’s add ions to the system to balance charges in the system.
+|| Let’s add ions to the system to balance charges.
 |-
@@ Line 410: / Line 410: @@
 || We don’t want to replace the atoms of the protein with ions.
-Choose '''13''' to replace solvent molecules for ions.
+I will choose '''13''' to replace solvent molecules for ions.
 |-
 || Scroll up and show the changes.
 || Notice that, the number of water molecules in the box have decreased.
 |-
@@ Line 423: / Line 425: @@
-* Solvent input files with coordinates
+* Solvent input files containing coordinates
 * Added solvent molecules with '''solvate''' command
 * About '''mdp''' file
@@ Line 450: / Line 452: @@
 '''Assignment'''
-|| From the '''Gromacs''' manual ,* Read on the following file extensions.
+|| From the '''Gromacs''' manual ,
 ** top, gro , mdp , tpr , itr
 * Create a table to keep track of which file gets generated in which step.

@@ Line 282: / Line 282: @@
 '''Gromacs''' also uses a '''mdp''' file, to assemble the system configuration.
-This file defines several parameters for the '''MD''' run.
+This file contains parameters required to assemble the system for '''MD''' run.
 Parameters such as time interval, number of steps or temperature are given.
 |-