Difference between revisions of "Protocol BCKDHA MD"
From Bioinformatikpedia
(→A brief check of results) |
(→Energy calculations) |
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* Potential: 9 |
* Potential: 9 |
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* Total Energy: 11 |
* Total Energy: 11 |
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| + | === Minimum distance between periodic boundary cells === |
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| + | It is important to calculate the minimal distances to find out if there are direct interactions. Such interactions could appear if the distances are shorter than the cut off value of electrostatic interactions. |
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| + | To calculate the minimum distance we used the command <br> |
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| + | <code> g_mindist -f wtMD.xtc -s wtMD.tpr -od minimal-periodic-distance.xvg -pi </code><br> |
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| + | After submitting this command we chose group 1 to calculate the minimum distance for the whole protein.<br> |
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Revision as of 14:53, 18 September 2011
Contents
This Protocol show how to analyse the data from molecular dynamics simulation
A brief check of results
To verified that the simulations finished properly we first use the command
gmxcheck -f wt.xtc
Quality assurance
Energy calculations
To calculate the different energies we used the command:
g_energy -f wtMD.edr -o energy.xvg
After submitting this command we had to choose the energy which should calculated.
- Pressure: 13
- Temperature: 12
- Potential: 9
- Total Energy: 11
Minimum distance between periodic boundary cells
It is important to calculate the minimal distances to find out if there are direct interactions. Such interactions could appear if the distances are shorter than the cut off value of electrostatic interactions.
To calculate the minimum distance we used the command
g_mindist -f wtMD.xtc -s wtMD.tpr -od minimal-periodic-distance.xvg -pi
After submitting this command we chose group 1 to calculate the minimum distance for the whole protein.
