Gromacs/C3/Temperature-and-Pressure-Equilibration/English - Revision history

Ranipv076 at 14:09, 21 February 2022

2022-02-21T14:09:08Z

2022-02-21T12:15:53Z

2022-02-21T10:00:14Z

2022-02-21T09:02:28Z

2022-02-18T09:10:35Z

2022-02-18T09:09:50Z

2022-02-18T09:06:49Z

2022-01-08T17:52:12Z

2022-01-08T17:47:38Z

2022-01-08T17:24:08Z

@@ Line 385: / Line 385: @@
 |-
 || Type, '''xmgrace pressure.xvg''' and press '''Enter'''.
-|| I will plot the '''dot''' '''xvg''' using '''Grace''' as seen.
+|| I will plot the '''pressure dot''' '''xvg''' using '''Grace''' as seen.
 Notice the fluctuations.

@@ Line 367: / Line 367: @@
 |-
 || Cursor on '''npt.gro'''.
-|| '''npt.gro''' is the output system from all the prior processes.
+|| '''npt.gro''' is the output system configuration from all the prior processes.
 |-

@@ Line 424: / Line 424: @@
 * Plot density and volume of the system after '''NVT''' and '''NPT''' steps.
-* Recap processes and commands from '''1AKI.pdb''' to equilibration.
+* Recap processes and commands starting from '''1AKI.pdb''' to equilibration.
 * Read publications of your choice using '''Gromacs'''.

@@ Line 412: / Line 412: @@
 * Ensemble properties and equilibration
-* Run '''NVT''' and temperature equilibration
+* Performed '''NVT''' and temperature equilibration
-* Plotted the temperature fluctuation to check for equilibration
+* Plotted the temperature fluctuation and checked for equilibration
 * '''NPT''' and pressure equilibration
 * Plotted the pressure fluctuation
@@ Line 426: / Line 426: @@
 * Recap processes and commands from '''1AKI.pdb''' to equilibration.
 * Read publications of your choice using '''Gromacs'''.
 |-

@@ Line 62: / Line 62: @@
 Notice the two mdp files provided.
-Copy the mdp files to the working directory.
+Copy the mdp file to the working directory.
 |-

@@ Line 108: / Line 108: @@
 Cursor on 50000 steps.
-|| This is a short simulation for 100 ps with each step having 2 fs.
+|| This is a short simulation for 100 ps with each step having 2 femtoseconds.
 Hence there are 50000 steps.

@@ Line 125: / Line 125: @@
 |-
 || Cursor on '''temperature''' and '''pcoupl '''parameters.
-|| Here, temperature is set to 300K.
+|| Here, temperature is set to 300 '''Kelvin'''.
@@ Line 253: / Line 253: @@
 Show files copied in the working directory.
-|| An additional file '''gro''' will be created at the completion of the process.
+|| An additional '''gro''' file will be created at the completion of the process.
 Copy the '''nvt''' files provided for analysis to continue further.
@@ Line 291: / Line 291: @@
 |-
 || Cursor on the graph.
-|| Notice that, the temperature fluctuates around 300 K.
+|| Notice that, the temperature fluctuates around 300 '''Kelvin'''.
 Velocity variation in the system is given by '''Maxwell-Boltzmann'''

@@ Line 214: / Line 214: @@
 '''Computation Time'''
-|| * Having more steps in MD takes longer time.
+||
 * Use a computing facility to run these processes.
 * Take care not to overheat or burn your computer.

← Older revision		Revision as of 17:47, 8 January 2022
Line 175:		Line 175:

	Pause the video and go through the additional materials section to know more.		Pause the video and go through the additional materials section to know more.
		+
		+	Go through the '''Gromacs''' manual for detailed understanding.

	\|-		\|-

@@ Line 136: / Line 136: @@
 |-
 || Show website at, [https://manual.gromacs.org/documentation/2019-current/reference-manual/special/remove-fast-dgf.html https://manual.gromacs.org/documentation/2019-current/reference-manual/special/remove-fast-dgf.html] '''
-|| Details on choosing them can be accessed from the '''Gromacs''' documentation.
+|| Details on choosing the parameters can be accessed from the '''Gromacs''' documentation.
 |-
@@ Line 172: / Line 172: @@
 |-
 || Cursor on the -r flag.
-|| The r flag is used only when position restraint is used in the '''mdp''' file.
+|| If the r flag is used, then position must be restrained.
-Go through the additional materials section to know more.
+Pause the video and go through the additional materials section to know more.
 |-