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Team:EPF-Lausanne/Modeling/RunSimulation
From 2009.igem.org
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==Theory== | ==Theory== | ||
The .pdb is generated from X-ray diffraction crystallography. This process requires a crystal of the protein, which occurs only at low temperature (~5°K). Taking this in consideration, we have to go through different steps to bring our protein to lab conditions. | The .pdb is generated from X-ray diffraction crystallography. This process requires a crystal of the protein, which occurs only at low temperature (~5°K). Taking this in consideration, we have to go through different steps to bring our protein to lab conditions. | ||
| + | |||
===Initial minimization=== | ===Initial minimization=== | ||
| - | We start with a few minimization rounds, to reach a minmimum in the | + | We start with a few minimization rounds, to reach a minmimum in the sense of potential energy. |
| + | |||
===Heating=== | ===Heating=== | ||
When the protein is stable, we have to add heat (kinetic energy) to reach an higher temperature (~300°K). We have to take a special care not to add heat too fast resulting in protein burst. | When the protein is stable, we have to add heat (kinetic energy) to reach an higher temperature (~300°K). We have to take a special care not to add heat too fast resulting in protein burst. | ||
| + | |||
===First NPT=== | ===First NPT=== | ||
This is a relaxation step, with constant atom number, pressure and temperature. This is a kind of homogeneization of the distribution of atoms inside our box. | This is a relaxation step, with constant atom number, pressure and temperature. This is a kind of homogeneization of the distribution of atoms inside our box. | ||
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===NVT=== | ===NVT=== | ||
This is also a relaxation step, with constant atom number, volume and temperature. | This is also a relaxation step, with constant atom number, volume and temperature. | ||
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===Second NPT=== | ===Second NPT=== | ||
Now we perform another relaxation NPT to reach lab conditions. | Now we perform another relaxation NPT to reach lab conditions. | ||
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===Final NPT=== | ===Final NPT=== | ||
This is the final NPT, which ast much longer and gives us the ouput of the simulation. | This is the final NPT, which ast much longer and gives us the ouput of the simulation. | ||
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===Initial minimization=== | ===Initial minimization=== | ||
This is quite easy to achieve, as NAMD has a specific keyword to run a simulation: minimize #OF_MINIMIZ_STEPS | This is quite easy to achieve, as NAMD has a specific keyword to run a simulation: minimize #OF_MINIMIZ_STEPS | ||
| + | |||
===Heating=== | ===Heating=== | ||
We tried different protocol, but this one is the best: | We tried different protocol, but this one is the best: | ||
Revision as of 09:30, 23 July 2009
Contents |
How to run a complete simulation
Theory
The .pdb is generated from X-ray diffraction crystallography. This process requires a crystal of the protein, which occurs only at low temperature (~5°K). Taking this in consideration, we have to go through different steps to bring our protein to lab conditions.
Initial minimization
We start with a few minimization rounds, to reach a minmimum in the sense of potential energy.
Heating
When the protein is stable, we have to add heat (kinetic energy) to reach an higher temperature (~300°K). We have to take a special care not to add heat too fast resulting in protein burst.
First NPT
This is a relaxation step, with constant atom number, pressure and temperature. This is a kind of homogeneization of the distribution of atoms inside our box.
NVT
This is also a relaxation step, with constant atom number, volume and temperature.
Second NPT
Now we perform another relaxation NPT to reach lab conditions.
Final NPT
This is the final NPT, which ast much longer and gives us the ouput of the simulation.
.conf file
Initial minimization
This is quite easy to achieve, as NAMD has a specific keyword to run a simulation: minimize #OF_MINIMIZ_STEPS
Heating
We tried different protocol, but this one is the best: reassignTemp $temp_step ;# starting temp reassignIncr $temp_step ;# temp increment reassignHold 300 ;# final temp reassignFreq 100 ;# num timesteps to temp incr.
