Simulations - Revision history

Oliver: -> bash script

2008-10-18T20:15:30Z

-> bash script

← Older revision		Revision as of 20:15, 18 October 2008
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	If there are problems, look at the <tt>log.txt</tt> output file.		If there are problems, look at the <tt>log.txt</tt> output file.

			Steps 1-4 can be automated with the bash script [[hippo_setup.sh]].

	[[Category:Hippo]]		[[Category:Hippo]]
	[[Category:Howto]]		[[Category:Howto]]

Oliver at 20:14, 18 October 2008

2008-10-18T20:14:09Z

← Older revision		Revision as of 20:14, 18 October 2008
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	The standard protocol is:		The standard protocol is:
	# make a working directory		# make a working directory
	# copy your input files (pdb and hippo_input.txt) into the working dir		# copy your input files (pdb and <tt>hippo_input.txt</tt>) into the working dir
	# copy the hippo data files (<tt>oplsaa_forcefield.dat</tt> and <tt>hippo_protein_database.dat</tt>) into the working dir		# copy the hippo data files (<tt>oplsaa_forcefield.dat</tt> and <tt>hippo_protein_database.dat</tt>) into the working dir
	# (optional) copy your executable into the working dir		# (optional) copy your executable into the working dir

Oliver at 20:13, 18 October 2008

2008-10-18T20:13:44Z

← Older revision		Revision as of 20:13, 18 October 2008
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	# make a working directory		# make a working directory
	# copy your input files (pdb and hippo_input.txt) into the working dir		# copy your input files (pdb and hippo_input.txt) into the working dir
	# (optional) copy your executable to the dir		# copy the hippo data files (<tt>oplsaa_forcefield.dat</tt> and <tt>hippo_protein_database.dat</tt>) into the working dir
			# (optional) copy your executable into the working dir
	# start hippo <pre>hippo</pre>		# start hippo <pre>hippo</pre>
	Hippo will load the pdb, build an internal topology, and then run the simulation. It will inform of its progress and its estimated finishing time.		Hippo will load the pdb, build an internal topology, and then run the simulation. It will inform of its progress and its estimated finishing time.

Oliver: basic outline of how to run simulations

2008-10-18T20:11:59Z

basic outline of how to run simulations

New page

This page should help you running simulations with [[Hippo]].

To run a simulation you will need
* hippo executable and data files in a directory which we will denote by HIPPO_HOME
* a pdb file for your system
* a [[Files#Command input file|hippo_input.txt]]

The standard protocol is:
# make a working directory
# copy your input files (pdb and hippo_input.txt) into the working dir
# (optional) copy your executable to the dir
# start hippo <pre>hippo</pre>
Hippo will load the pdb, build an internal topology, and then run the simulation. It will inform of its progress and its estimated finishing time.

If there are problems, look at the <tt>log.txt</tt> output file.

[[Category:Hippo]]
[[Category:Howto]]