-
Notifications
You must be signed in to change notification settings - Fork 1
/
Copy pathlec6
78 lines (52 loc) · 3.11 KB
/
lec6
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
After molecular dynamics simulation, its time for analysis. This step basically examines various parameters like:
1) Temperature flactuation the protein went through during the temperature equilibration simulation.
2) Pressure flactuation the protein went through during the pressure equilibration simulation.
3) RMSD (Root Mean Square Daviation) of the backbone atoms during the MDS (molecular dynamic simulation) run.
4) RMSF (Root Mean Square Fluctuation) of the backbone atoms during the MDS run.
5) ROG (Radious of Gyration) of the protein molecule.
6) Hydrogen bonding calculation.
7) Van der Waals interaction calculatiion.
Only 1-3 has been discussed in the current lecutre, other will be discussed in an extension file to this lecture.
1) Plotting the temperature variation:
--------------------------------------
Command:
$ gmx energy -f nvt.edr -o temp.xvg
Here,
energy This module reads through the .edr file (portable energy file), and organizes temperature vs time data to a .xvg file.
-f nvt.edr '-f' option indicates which file will be the input of the energy module
-o temp.xvg '-o' option specifies the output filename as usual.
During this run, the option 16) Temperaure is selected.
2) Plotting the pressure variation:
-----------------------------------
Command:
$ gmx energy -f npt.edr -o pressure.xvg
This is basically the same command as the previous one, except for preesure instead of temperature. The option 18) Pressure is selected in this run.
2.5) Converting MDS trajectory
------------------------------
This is an intermediate step that enables calculating all the derived quantities like RMSD, RMSF, ROG etc possible. The command:
$ gmx trjconv -s md1.tpr -f md1.xtc -o neoMd.xtc -pbc mol -center
Here,
trjconv The module that convert MD trajectory information to .xtc (portable trajectory) file.
-s md1.tpr -s specifies the .tpr file.
-f md1.xtc -f specifies the .xtc file.
-pbc mol center 'pbc' stands for Periodic Boundary Condition.
During this run, 1) Protein was selected with respect to 0) System.
3) RMSD of the backbone atom:
-----------------------------
Command:
$ gmx rms -s md1.tpr -f neoMd.xtc -o rmsd.xvg
Here,
rms The module that calculates RMSD, RMSF and other related quantites.
-s md1.tpr The binary file containing the final MDS parameters.
-f neoMd.xtc Portable MDS trajectory file, specified as another input of rms module using '-f' command.
-o rmsd.xvg Specifying the output file.
The RMSD was calculated for the backbone (option 4) against the backbone.
==============================
In addition, the MDS trajectory file can be used to generate a .pdb file that visualizes the protein after simulation and all the treatment leading to it. The
command related to it is:
$ gmx editconf -f md1.gro -o md1_1aki.pdb
As can be seen, here,
editconf The module that is gonna consume .gro file and spit out the .pdb file.
-f md1.gro The input file have to be a .gro file, here the .gro file of MDS - md1.gro.
-o md1_1aki.pdb The output file.
Visually inspecting the protien, though not a quantitative analysis, provides a intutive analysis.