Difference between revisions of "Cluster:Pymol"
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| − | Once you have run: | + | Once you have run: <tt>grompp -f file.mdp -p topol.top -o file.tpr</tt> |
| − | <tt>grompp -f file.mdp -p topol.top -o file.tpr</tt> | + | <p>Which takes in a run configuration mdp file, and a system topology file, topol.top and outputs a tpr file.</p> |
| − | Which takes in a run configuration mdp file, and a system topology file, topol.top and outputs a tpr file. | + | <p>And after running the simulation: <tt>mdrun -deffnm run</tt></p> |
| − | And after | + | <p>Convert the gromacs trajectory file to a pdb file: <tt>trjconv -s run.topr -f lowpass.xtc -o file.pdb</tt></p> |
| − | <tt>mdrun -deffnm run</tt> | ||
| − | Convert the gromacs trajectory file to a pdb file | ||
| − | <tt>trjconv -s run.topr -f lowpass.xtc -o file.pdb</tt> | ||
In order to just view the molecule being simulated select protein for the output group. | In order to just view the molecule being simulated select protein for the output group. | ||
| − | Run pymol on the created pdb file | + | <p>Run pymol on the created pdb file: <tt>pymol file.pdb</tt></p> |
| − | <tt>pymol file.pdb</tt> | + | Control pymol with the VCR buttons |
Revision as of 13:13, 25 May 2005
Once you have run: grompp -f file.mdp -p topol.top -o file.tpr
Which takes in a run configuration mdp file, and a system topology file, topol.top and outputs a tpr file.
And after running the simulation: mdrun -deffnm run
Convert the gromacs trajectory file to a pdb file: trjconv -s run.topr -f lowpass.xtc -o file.pdb
In order to just view the molecule being simulated select protein for the output group.
Run pymol on the created pdb file: pymol file.pdb
Control pymol with the VCR buttons
