Cluster:Pymol - Revision history

Lemanal at 18:32, 25 May 2005

2005-05-25T18:32:56Z

← Older revision		Revision as of 18:32, 25 May 2005
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	<p>Once you have run:<br>		<p>Once you have run:<br>
	<tt>grompp -f ~~file~~.mdp -p topol.top -o ~~file~~.tpr</tt><br>		<tt>grompp -f run.mdp -p topol.top -o run.tpr</tt><br>
	Which takes as parameters a run configuration mdp file and a system topology file, topol.top and outputs a tpr file.</p>		Which takes as parameters a run configuration mdp file and a system topology file, topol.top and outputs a tpr file.</p>

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	<p>Run pymol on the created pdb file:<br>		<p>Run pymol on the created pdb file:<br>
	<tt>pymol ~~file~~.pdb</tt><br>		<tt>pymol run.pdb</tt><br>
	Control pymol with the VCR buttons</p>		Control pymol with the VCR buttons</p>

Lemanal at 18:26, 25 May 2005

2005-05-25T18:26:32Z

← Older revision		Revision as of 18:26, 25 May 2005
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	<br>		<br>
	<p>		<p>
	Adapted from Erik Lindahl's ''Paralellel Molecular Dynamics: Gromacs'', Cluster World, Vol 2 No 8, 2004.		Adapted from Erik Lindahl's ''Paralellel Molecular Dynamics: Gromacs'', Cluster World Vol 2 No 8, 2004.

Lemanal at 18:26, 25 May 2005

2005-05-25T18:26:11Z

← Older revision		Revision as of 18:26, 25 May 2005
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	<tt>pymol file.pdb</tt><br>		<tt>pymol file.pdb</tt><br>
	Control pymol with the VCR buttons</p>		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.

Lemanal at 18:23, 25 May 2005

2005-05-25T18:23:30Z

← Older revision		Revision as of 18:23, 25 May 2005
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	In order to view just the molecule being modeled select protein for the output group.</p>		In order to view just the molecule being modeled select protein for the output group.</p>

	<p>Run pymol on the created pdb file: <tt>pymol file.pdb</tt><br>		<p>Run pymol on the created pdb file:<br>
			<tt>pymol file.pdb</tt><br>
	Control pymol with the VCR buttons</p>		Control pymol with the VCR buttons</p>

Lemanal at 18:22, 25 May 2005

2005-05-25T18:22:40Z

← Older revision		Revision as of 18:22, 25 May 2005
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	Once you have run: <tt>grompp -f file.mdp -p topol.top -o file.tpr</tt>		<p>Once you have run:<br>
	<p>Which takes in a run configuration mdp file, and a system topology file, topol.top and outputs a tpr file.</p>		<tt>grompp -f file.mdp -p topol.top -o file.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></p>
	In order to just ~~view~~ the molecule being ~~simulated~~ select protein for the output group.		<p>And after running the simulation:<br>
	<p>Run pymol on the created pdb file: <tt>pymol file.pdb</tt></p>		<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: <tt>pymol file.pdb</tt><br>
			Control pymol with the VCR buttons</p>

Lemanal at 18:13, 25 May 2005

2005-05-25T18:13:55Z

← Older revision		Revision as of 18:13, 25 May 2005
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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 ~~starting~~ the simulation:		<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

Lemanal at 18:08, 25 May 2005

2005-05-25T18:08:16Z

New page

Once you have run:
<tt>grompp -f file.mdp -p topol.top -o file.tpr</tt>
Which takes in a run configuration mdp file, and a system topology file, topol.top and outputs a tpr file.
And after starting the simulation:
<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.
Run pymol on the created pdb file.
<tt>pymol file.pdb</tt>