Difference between revisions of "Molecular Dynamics Analysis BCKDHA"
From Bioinformatikpedia
(→How long did the simulation run in real time (hours), what was the simulation speed (ns/day) and how many years would the simulation take to reach a second?) |
(→Visualization of results) |
||
Line 14: | Line 14: | ||
== Visualization of results == |
== Visualization of results == |
||
+ | |||
+ | To visualize the topology and trajectory we use the trajectory viewer supplied with gromacs. |
||
+ | |||
+ | <code> ngmx -s wt.tpr -f wt.xtc </code> |
||
== Quality assurance == |
== Quality assurance == |
Revision as of 14:28, 26 August 2011
Contents
- 1 A brief check of results
- 1.1 How many frames are in the trajectory file and what is the time resolution?
- 1.2 How long did the simulation run in real time (hours), what was the simulation speed (ns/day) and how many years would the simulation take to reach a second?
- 1.3 Which contribution to the potential energy accounts for most of the calculations?
- 2 Visualization of results
- 3 Quality assurance
A brief check of results
To verified that the simulations finished properly we first use the command
gmxcheck -f wt.xtc
How many frames are in the trajectory file and what is the time resolution?
How long did the simulation run in real time (hours), what was the simulation speed (ns/day) and how many years would the simulation take to reach a second?
- real time: 9h27:35
- simulation speed: 25.370 ns/day
- simulation speed: 107991 years/second
Which contribution to the potential energy accounts for most of the calculations?
Visualization of results
To visualize the topology and trajectory we use the trajectory viewer supplied with gromacs.
ngmx -s wt.tpr -f wt.xtc