Hippo - Revision history

Kaihsu: /* Features */

2008-11-13T13:49:05Z

Features

← Older revision		Revision as of 13:49, 13 November 2008
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	== Features ==		== Features ==
			[[Image:Hippopotamus.jpg\|thumb\|right\|Not this hippo.]]
	=== Simulation methods ===		=== Simulation methods ===
	* [[Molecular dynamics]] (MD) in NVT, NPT, NVE ensembles <cite>Proteins2008</cite>		* [[Molecular dynamics]] (MD) in NVT, NPT, NVE ensembles <cite>Proteins2008</cite>

Oliver: added latest U&U paper

2008-10-20T22:47:39Z

added latest U&U paper

← Older revision		Revision as of 22:47, 20 October 2008
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	== Features ==		== Features ==
	=== Simulation methods ===		=== Simulation methods ===
	* [[Molecular dynamics]] (MD) in NVT, NPT, NVE ensembles		* [[Molecular dynamics]] (MD) in NVT, NPT, NVE ensembles <cite>Proteins2008</cite>
	* Metropolis [[Monte Carlo]] (MC) in NVT and NPT ensembles <cite>JACS2004,JPhysChemB2006</cite>		* Metropolis [[Monte Carlo]] (MC) in NVT and NPT ensembles <cite>JACS2004,JPhysChemB2006</cite>
	* [[Replica exchange]] with MD and MC		* [[Replica exchange]] with MD and MC <cite>Proteins2007</cite>

	=== Force fields ===		=== Force fields ===
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	* explicit solvent (water: TIP4P <cite>Jorgensen1985</cite>, SPC <cite>Berendsen1981</cite>)		* explicit solvent (water: TIP4P <cite>Jorgensen1985</cite>, SPC <cite>Berendsen1981</cite>)
	* Generalized Born implicit solvent (GB/SA)		* Generalized Born implicit solvent (GB/SA)
	* Generalized Born implicit membrane (GB/IM) <cite>Proteins2007,BJ2007,Proteins2005</cite>		* Generalized Born implicit membrane (GB/IM) <cite>Proteins2008,Proteins2007,BJ2007,Proteins2005</cite>

	=== Enhanced productivity ===		=== Enhanced productivity ===
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	#Cordes2002 pmid=12417206		#Cordes2002 pmid=12417206
	#Daura1999 X Daura, K Gademann, B Jaun, D Seebach, WF van Gunsteren, and AE Mark. ''Peptide folding: When simulation meets experiment''. Angewandte Chemie-International Edition, 38 (1-2):236–240, 1999. [http://dx.doi.org/10.1002/(SICI)1521-3773(19990115)38:1/2%3C236::AID-ANIE236%3E3.0.CO;2-M <nowiki>10.1002/(SICI)1521-3773(19990115)38:1/2<236::AID-ANIE236>3.0.CO;2-M</nowiki>].		#Daura1999 X Daura, K Gademann, B Jaun, D Seebach, WF van Gunsteren, and AE Mark. ''Peptide folding: When simulation meets experiment''. Angewandte Chemie-International Edition, 38 (1-2):236–240, 1999. [http://dx.doi.org/10.1002/(SICI)1521-3773(19990115)38:1/2%3C236::AID-ANIE236%3E3.0.CO;2-M <nowiki>10.1002/(SICI)1521-3773(19990115)38:1/2<236::AID-ANIE236>3.0.CO;2-M</nowiki>].
			#Proteins2008 Jakob P. Ulmschneider and Martin B. Ulmschneider. ''Sampling efficiency in explicit and implicit membrane environments studied by peptide folding simulations''. Proteins [http://dx.doi.org/10.1002/prot.22270 10.1002/prot.22270].
	</biblio>		</biblio>

	[[Category:Hippo]]		[[Category:Hippo]]
	[[Category:Software]]		[[Category:Software]]

Oliver: /* Installing the software */ OpenMP link

2008-10-19T15:44:06Z

Installing the software: OpenMP link

← Older revision		Revision as of 15:44, 19 October 2008
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	In this case try the <tt>hippo_p3</tt> or <tt>hippo_p3.exe</tt> executable. If this still doesn't work, [http://forums.biowerkzeug.org/viewforum.php?f=6 post a request in the Hippo Installation forum].		In this case try the <tt>hippo_p3</tt> or <tt>hippo_p3.exe</tt> executable. If this still doesn't work, [http://forums.biowerkzeug.org/viewforum.php?f=6 post a request in the Hippo Installation forum].

	Executables with the <tt>_mpi</tt> extension have been compiled with MPI support ([http://www.mcs.anl.gov/research/projects/mpich2/index.php mpich2]) and are only used for [[replica exchange simulations]] (REXMD). If you just want to run multithreaded simulations just use the standard binaries (which are all compiled with OpenMP).		Executables with the <tt>_mpi</tt> extension have been compiled with MPI support ([http://www.mcs.anl.gov/research/projects/mpich2/index.php mpich2]) and are only used for [[replica exchange simulations]] (REXMD). If you just want to run multithreaded simulations just use the standard binaries (which are all compiled with [http://www.openmp.org/ OpenMP]).

	=== Test cases ===		=== Test cases ===

Oliver: /* Installing the software */

2008-10-19T15:42:51Z

Installing the software

← Older revision		Revision as of 15:42, 19 October 2008
Line 70:		Line 70:
	In this case try the <tt>hippo_p3</tt> or <tt>hippo_p3.exe</tt> executable. If this still doesn't work, [http://forums.biowerkzeug.org/viewforum.php?f=6 post a request in the Hippo Installation forum].		In this case try the <tt>hippo_p3</tt> or <tt>hippo_p3.exe</tt> executable. If this still doesn't work, [http://forums.biowerkzeug.org/viewforum.php?f=6 post a request in the Hippo Installation forum].

	Executables with the <tt>_mpi</tt> extension have been compiled with MPI support ([http://www.mcs.anl.gov/research/projects/mpich2/index.php mpich2]) and are only used for replica exchange ~~simulation~~ (REXMD). If you just want to run multithreaded simulations just use the standard binaries (which are all compiled with OpenMP).		Executables with the <tt>_mpi</tt> extension have been compiled with MPI support ([http://www.mcs.anl.gov/research/projects/mpich2/index.php mpich2]) and are only used for [[replica exchange simulations]] (REXMD). If you just want to run multithreaded simulations just use the standard binaries (which are all compiled with OpenMP).

	=== Test cases ===		=== Test cases ===

Oliver: /* Installing the software */ mpich2 link

2008-10-19T15:42:13Z

Installing the software: mpich2 link

← Older revision		Revision as of 15:42, 19 October 2008
Line 70:		Line 70:
	In this case try the <tt>hippo_p3</tt> or <tt>hippo_p3.exe</tt> executable. If this still doesn't work, [http://forums.biowerkzeug.org/viewforum.php?f=6 post a request in the Hippo Installation forum].		In this case try the <tt>hippo_p3</tt> or <tt>hippo_p3.exe</tt> executable. If this still doesn't work, [http://forums.biowerkzeug.org/viewforum.php?f=6 post a request in the Hippo Installation forum].

	Executables with the <tt>_mpi</tt> extension have been compiled with MPI support (~~mpich 2~~) and are only used for replica exchange simulation (REXMD). If you just want to run multithreaded simulations just use the standard binaries (which are all compiled with OpenMP).		Executables with the <tt>_mpi</tt> extension have been compiled with MPI support ([http://www.mcs.anl.gov/research/projects/mpich2/index.php mpich2]) and are only used for replica exchange simulation (REXMD). If you just want to run multithreaded simulations just use the standard binaries (which are all compiled with OpenMP).

	=== Test cases ===		=== Test cases ===

Oliver: /* Installing the software */ clarified MPI binaries (after talking to Martin)

2008-10-19T15:19:56Z

Installing the software: clarified MPI binaries (after talking to Martin)

← Older revision		Revision as of 15:19, 19 October 2008
Line 70:		Line 70:
	In this case try the <tt>hippo_p3</tt> or <tt>hippo_p3.exe</tt> executable. If this still doesn't work, [http://forums.biowerkzeug.org/viewforum.php?f=6 post a request in the Hippo Installation forum].		In this case try the <tt>hippo_p3</tt> or <tt>hippo_p3.exe</tt> executable. If this still doesn't work, [http://forums.biowerkzeug.org/viewforum.php?f=6 post a request in the Hippo Installation forum].

	Executables with the <tt>_mpi</tt> extension have been compiled with ~~OpenMP~~ and ~~can~~ run ~~on multiple CPUs. However, not~~ all ~~code segments are yet parallelized~~.		Executables with the <tt>_mpi</tt> extension have been compiled with MPI support (mpich 2) and are only used for replica exchange simulation (REXMD). If you just want to run multithreaded simulations just use the standard binaries (which are all compiled with OpenMP).

	=== Test cases ===		=== Test cases ===

Oliver: /* Installing the software */

2008-10-17T22:09:02Z

Installing the software

← Older revision		Revision as of 22:09, 17 October 2008
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	* compiled executables (see below)		* compiled executables (see below)
	** <tt>hippo</tt>: the [[#Simulation methods\|MD and MC program]]		** <tt>hippo</tt>: the [[#Simulation methods\|MD and MC program]]
	** <tt>analyse</tt>: the[[#Analysis\|analysis program]]		** <tt>analyse</tt>: the [[#Analysis\|analysis program]]
	* the manual ([http://www.biowerkzeug.de/downloads/hippo/hippo_manual.pdf pdf])		* the manual ([http://www.biowerkzeug.de/downloads/hippo/hippo_manual.pdf pdf])
	* the [[Hippo license\|license]] (to which you consent by downloading)		* the [[Hippo license\|license]] (to which you consent by downloading)

Oliver: /* Installing the software */ links

2008-10-17T22:08:39Z

Installing the software: links

← Older revision		Revision as of 22:08, 17 October 2008
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	Unzip the downloaded file. It will unpack into its own <tt>hippo</tt> directory where you will find		Unzip the downloaded file. It will unpack into its own <tt>hippo</tt> directory where you will find
	* compiled executables (see below)		* compiled executables (see below)
	** <tt>hippo</tt>: the MD and MC program		** <tt>hippo</tt>: the [[#Simulation methods\|MD and MC program]]
	** <tt>analyse</tt>: the analysis program		** <tt>analyse</tt>: the[[#Analysis\|analysis program]]
	* the manual ([http://www.biowerkzeug.de/downloads/hippo/hippo_manual.pdf pdf])		* the manual ([http://www.biowerkzeug.de/downloads/hippo/hippo_manual.pdf pdf])
	* the [[Hippo license\|license]] (to which you consent by downloading)		* the [[Hippo license\|license]] (to which you consent by downloading)

Oliver: /* Installing the software */ floating table

2008-10-17T22:06:54Z

Installing the software: floating table

← Older revision		Revision as of 22:06, 17 October 2008
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	* the <tt>testjobs</tt> directory with example systems		* the <tt>testjobs</tt> directory with example systems

	The package includes binaries that run under Linux and Windows on any Intel or AMD processor that has the SSE or SSSE3 multi media instructions. Depending on your system and needs, choose the an executable from the package as shown in the table:		{\| class="wikitable" align="right"

	{\| class="wikitable"
	\|+Hippo executables		\|+Hippo executables
	!cpu !!Linux !!Windows		!cpu !!Linux !!Windows
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	\|SSE (PIII,P4,Athlon,...) \|\|<tt>hippo_p3</tt> \|\|<tt>hippo_p3.exe</tt>		\|SSE (PIII,P4,Athlon,...) \|\|<tt>hippo_p3</tt> \|\|<tt>hippo_p3.exe</tt>
	\|}		\|}

			The package includes binaries that run under Linux and Windows on any Intel or AMD processor that has the SSE or SSSE3 multi media instructions. Depending on your system and needs, choose an executable from the package as shown in the table ''Hippo executables''.

	If in doubt, simply try them out in order; if it will not run you will receive an error message such as		If in doubt, simply try them out in order; if it will not run you will receive an error message such as

Oliver: /* Installing the software */

2008-10-17T22:05:00Z

Installing the software

← Older revision		Revision as of 22:05, 17 October 2008
Line 42:		Line 42:

	=== Installing the software ===		=== Installing the software ===

	Unzip the downloaded file. It will unpack into its own <tt>hippo</tt> directory where you will find		Unzip the downloaded file. It will unpack into its own <tt>hippo</tt> directory where you will find
	* compiled executables (see below)		* compiled executables (see below)
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	* the <tt>testjobs</tt> directory with example systems		* the <tt>testjobs</tt> directory with example systems

	The package includes binaries that run under Linux and Windows on any Intel or AMD processor that has the SSE or SSSE3 multi media instructions. Depending on your system and needs, choose the ~~following~~ executable from the package:		The package includes binaries that run under Linux and Windows on any Intel or AMD processor that has the SSE or SSSE3 multi media instructions. Depending on your system and needs, choose the an executable from the package as shown in the table:

	{\|		{\| class="wikitable"
	\|+Hippo executables		\|+Hippo executables
	!cpu !!Linux !!Windows		!cpu !!Linux !!Windows
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	\|SSE (PIII,P4,Athlon,...) \|\|<tt>hippo_p3</tt> \|\|<tt>hippo_p3.exe</tt>		\|SSE (PIII,P4,Athlon,...) \|\|<tt>hippo_p3</tt> \|\|<tt>hippo_p3.exe</tt>
	\|}		\|}


	If in doubt, simply try them out in order; if it will not run you will receive an error message such as		If in doubt, simply try them out in order; if it will not run you will receive an error message such as