Gromacs/C3/Production-Run-for-Lysozyme/English - Revision history

Ranipv076 at 08:12, 6 June 2022

2022-06-06T08:12:04Z

Snehalathak at 06:52, 6 June 2022

2022-06-06T06:52:29Z

Snehalathak at 06:42, 6 June 2022

2022-06-06T06:42:41Z

Ranipv076 at 08:26, 30 May 2022

2022-05-30T08:26:22Z

Ranipv076 at 08:17, 30 May 2022

2022-05-30T08:17:38Z

Ranipv076 at 07:36, 30 May 2022

2022-05-30T07:36:17Z

Ranipv076 at 07:33, 30 May 2022

2022-05-30T07:33:41Z

Ranipv076 at 07:32, 30 May 2022

2022-05-30T07:32:28Z

Ranipv076 at 07:31, 30 May 2022

2022-05-30T07:31:58Z

Snehalathak at 07:27, 26 May 2022

2022-05-26T07:27:00Z

@@ Line 140: / Line 140: @@
 |-
 || '''Slide Number 9'''
 '''Timescale of Protein Motions'''
@@ Line 252: / Line 261: @@
 |-
-|| '''Slide Number 9'''
+|| '''Slide Number 11'''
 '''Data Analysis'''
@@ Line 462: / Line 471: @@
 |-
-|| '''Slide Number 10'''
+|| '''Slide Number 12'''
 '''Summary '''
@@ Line 473: / Line 482: @@
 |-
-|| '''Slide Number 11'''
+|| '''Slide Number 13'''
 '''Summary'''
@@ Line 481: / Line 490: @@
 |-
-|| '''Slide Number 12'''
+|| '''Slide Number 14'''
 '''Assignment'''
@@ Line 491: / Line 500: @@
 |-
-|| '''Slide Number 13'''
+|| '''Slide Number 15'''
 '''Assignment'''
@@ Line 500: / Line 509: @@
 |-
-|| '''Slide Number 14'''
+|| '''Slide Number 16'''
 '''Spoken Tutorial Project'''
@@ Line 508: / Line 517: @@
 |-
-|| '''Slide Number 15'''
+|| '''Slide Number 17'''
 '''Spoken Tutorial workshops'''
@@ Line 516: / Line 525: @@
 |-
-|| '''Slide Number 15'''
+|| '''Slide Number 18'''
 '''Forum for questions'''
@@ Line 522: / Line 531: @@
 |-
-|| '''Slide Number 16'''
+|| '''Slide Number 19'''
 '''Acknowledgment'''

@@ Line 276: / Line 276: @@
 Atomic interactions, kinetics and '''PCA''' are also options.
-These are useful to analyze flexible structures or ones such as molten globules.
+These are useful to analyze flexible structures or molten globules.
 |-

@@ Line 134: / Line 134: @@
 '''Timescale of Protein Motions'''
 ||
-* In microsecond or millisecond, ligand binding or folding is studied.
+* In microsecond or millisecond timescale, ligand binding or folding is studied.
 * These are computationally intensive processes
 * Use a high performance computation facility or a '''GPU''' for longer calculations

@@ Line 405: / Line 405: @@
 Go to '''representations''' and click on '''Create Rep'''.
-|| Let’s close this window.
+|| Go to '''representations''' window and create a new representation.
-−
 Go to '''representations''' window and create a new representation.
 |-
@@ Line 464: / Line 462: @@
 |-
-|| '''Slide Number 9'''
+|| '''Slide Number 10'''
 '''Summary '''
@@ Line 475: / Line 473: @@
 |-
-|| '''Slide Number 10'''
+|| '''Slide Number 11'''
 '''Summary'''
@@ Line 483: / Line 481: @@
 |-
-|| '''Slide Number 11'''
+|| '''Slide Number 12'''
 '''Assignment'''
@@ Line 489: / Line 487: @@
 * Open the '''log''' file and go through the details
-* Plot '''RMSD''' of '''trace''' (C-alpha) atoms only
+* Plot '''RMSD''' of '''trace''' (C-alpha) atoms
 * Create '''Ramachandran''' plot of the lowest and highest energy structure
 |-
-|| '''Slide Number 12'''
+|| '''Slide Number 13'''
 '''Assignment'''
@@ Line 502: / Line 500: @@
 |-
-|| '''Slide Number 13'''
+|| '''Slide Number 14'''
 '''Spoken Tutorial Project'''
@@ Line 510: / Line 508: @@
 |-
-|| '''Slide Number 14'''
+|| '''Slide Number 15'''
 '''Spoken Tutorial workshops'''

@@ Line 135: / Line 135: @@
 ||
 * In microsecond or millisecond, ligand binding or folding is studied.
-* These are computationally intensive processes.
+* These are computationally intensive processes
-* Use a high performance computation facility or a '''GPU''' for longer calculations.
+* Use a high performance computation facility or a '''GPU''' for longer calculations
 |-
 || Go to the '''terminal'''.
 || Go to the '''terminal'''.
 |-
@@ Line 150: / Line 153: @@
 || Enter the command as seen here to assemble the '''configuration''' for the '''md''' run.
-'''npt.gro is''' the starting structure for the production md run.
+'''npt.gro is''' the starting structure for the '''production md run'''.
 |-
@@ Line 156: / Line 159: @@
 || The '''tpr''' file is the output file from this step.
-An '''-r''' flag is used if we need to restrain the protein conformation.
+An '''r''' flag is used if we need to restrain the protein conformation.
 This is often done when studying protein-ligand binding.
@@ Line 179: / Line 182: @@
 |-
-|| Type,
+|| Type, '''gmx mdrun -v -deffnm md-1''' and press '''Enter'''.
-−
 '''gmx mdrun -v -deffnm md-1''' and press '''Enter'''.
 || Enter the '''mdrun''' command as seen to start the '''production run'''.
@@ Line 275: / Line 276: @@
 Atomic interactions, kinetics and '''PCA''' are also options.
-These are useful to analyse flexible structures or ones such as molten globules.
+These are useful to analyze flexible structures or ones such as molten globules.
 |-
@@ Line 299: / Line 300: @@
 '''Windows''' users must first open '''VMD'''.
-Then open the '''gro''' file, followed by the '''xtc''' '''trajectory''' file.
+Then open the '''gro''' file, followed by the '''xtc '''trajectory''' file.
 |-

@@ Line 52: / Line 52: @@
 '''Code Files'''
-|| * Files used in this tutorial are provided in the '''code files''' link.
+||
 * Please download and extract the files.
 * Make a copy and then use them while practising.

@@ Line 24: / Line 24: @@
 '''Learning Objectives'''
-|| * Save data to various output files
+||
 * Align a frame in the trajectory with a reference molecule

@@ Line 36: / Line 36: @@
 * '''Gromacs''' v2021.2
 * '''VMD''' 1.9.3
 |-

@@ Line 14: / Line 14: @@
 '''Learning Objectives'''
 || In this tutorial, we will,
-* Complete 1ns production run for '''lysozyme'''
+* Complete 1 nanosecond production run for '''lysozyme'''
 * About timescales of motions
 * Time taken for simulation