Difference between revisions of "Cluster:Pymol"
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| − | Once you have run: <tt>grompp -f | + | <p>Once you have run:<br> |
| − | < | + | <tt>grompp -f run.mdp -p topol.top -o run.tpr</tt><br> |
| − | <p>And after running the simulation: <tt>mdrun -deffnm run</tt></p> | + | Which takes as parameters a run configuration mdp file and a system topology file, topol.top and outputs a tpr file.</p> |
| − | <p>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 | + | <p>And after running the simulation:<br> |
| − | <p>Run pymol on the created pdb file: <tt>pymol | + | <tt>mdrun -deffnm run</tt></p> |
| − | Control pymol with the VCR buttons | + | |
| + | <p>Run the mdrun output through a lowpass filter to smooth out the transition of the atoms in the system between time steps:<br> | ||
| + | <tt>g_filter -s run.tpr -f run.xtc -ol lowpass.xtc -nx 10 -all</tt></p> | ||
| + | |||
| + | <p>Convert the gromacs trajectory file to a pdb file:<br> | ||
| + | <tt>trjconv -s run.topr -f lowpass.xtc -o file.pdb</tt><br> | ||
| + | In order to view just the molecule being modeled select protein for the output group.</p> | ||
| + | |||
| + | <p>Run pymol on the created pdb file:<br> | ||
| + | <tt>pymol run.pdb</tt><br> | ||
| + | Control pymol with the VCR buttons</p> | ||
| + | |||
| + | <br> | ||
| + | <p> | ||
| + | Adapted from Erik Lindahl's ''Paralellel Molecular Dynamics: Gromacs'', Cluster World Vol 2 No 8, 2004. | ||
Latest revision as of 13:32, 25 May 2005
Once you have run:
grompp -f run.mdp -p topol.top -o run.tpr
Which takes as parameters 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
Run the mdrun output through a lowpass filter to smooth out the transition of the atoms in the system between time steps:
g_filter -s run.tpr -f run.xtc -ol lowpass.xtc -nx 10 -all
Convert the gromacs trajectory file to a pdb file:
trjconv -s run.topr -f lowpass.xtc -o file.pdb
In order to view just the molecule being modeled select protein for the output group.
Run pymol on the created pdb file:
pymol run.pdb
Control pymol with the VCR buttons
Adapted from Erik Lindahl's Paralellel Molecular Dynamics: Gromacs, Cluster World Vol 2 No 8, 2004.
