GROMACS - Revision history

145.118.87.250: /* Force fields */

2021-10-14T13:30:02Z

Force fields

← Older revision		Revision as of 15:30, 14 October 2021
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	GROMACS can use either the [[SHAKE]] or the [[LINCS]] algorithms <ref>[http://www.gromacs.org/@api/deki/files/82/=gromacs4_manual.pdf GROMACS 4 Manual] § 3.6 </ref>.		GROMACS can use either the [[SHAKE]] or the [[LINCS]] algorithms <ref>[http://www.gromacs.org/@api/deki/files/82/=gromacs4_manual.pdf GROMACS 4 Manual] § 3.6 </ref>.
	==Force fields==		==Force fields==
	~~GRMACS~~ comes with the following [[force fields]] <ref>Source: /usr/share/gromacs/top for gromacs-4.5.5 </ref><ref>GROMACS 4.5.6 manual § 4.10 </ref>		GROMACS comes with the following [[force fields]] <ref>Source: /usr/share/gromacs/top for gromacs-4.5.5 </ref><ref>GROMACS 4.5.6 manual § 4.10 </ref>
	* [[AMBER forcefield \| AMBER]]		* [[AMBER forcefield \| AMBER]]
	** amber03		** amber03

Carl McBride: /* Force fields */ Started adding references

2013-11-07T12:12:06Z

Force fields: Started adding references

← Older revision		Revision as of 14:12, 7 November 2013
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	GRMACS comes with the following [[force fields]] <ref>Source: /usr/share/gromacs/top for gromacs-4.5.5 </ref><ref>GROMACS 4.5.6 manual § 4.10 </ref>		GRMACS comes with the following [[force fields]] <ref>Source: /usr/share/gromacs/top for gromacs-4.5.5 </ref><ref>GROMACS 4.5.6 manual § 4.10 </ref>
	* [[AMBER forcefield \| AMBER]]		* [[AMBER forcefield \| AMBER]]
	** amber03		** amber03
	** amber94		** amber94 <ref>[http://dx.doi.org/10.1021/ja00124a002 Wendy D. Cornell , Piotr Cieplak , Christopher I. Bayly , Ian R. Gould , Kenneth M. Merz , David M. Ferguson , David C. Spellmeyer , Thomas Fox , James W. Caldwell , Peter A. Kollman "A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules", Journal of the American Chemical Society (JACS) '''117''' pp. 5179-5197 (1995)]</ref>
	** amber96		** amber96
	** amber99		** amber99
	** amber99sb		** amber99sb
	** amber99sb-ildn		** amber99sb-ildn
	** amberGS		** amberGS <ref>[http://dx.doi.org/10.1073/pnas.042496899 Angel E. García and Kevin Y. Sanbonmatsu "α-Helical stabilization by side chain shielding of backbone hydrogen bonds", PNAS '''99''' pp. 2782-2787 (2002)]</ref>

	*[[CHARMM]]		*[[CHARMM]]
	** charmm27		** charmm27
	*[[ENCAD (force field) \| ENCAD]]		*[[ENCAD (force field) \| ENCAD]]
	** encads		** encads (full solvent charges)
	** encadv		** encadv (scaled-down vacuum charges)
	*[[GROMOS]]		*[[GROMOS]]
	** gromos43a1		** gromos43a1

Carl McBride: /* Force fields */

2013-11-05T17:19:11Z

Force fields

← Older revision		Revision as of 19:19, 5 November 2013
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	** encads		** encads
	** encadv		** encadv
	* gmx2
	* gmx
	*[[GROMOS]]		*[[GROMOS]]
	** gromos43a1		** gromos43a1

Carl McBride: Added a force fields section

2013-11-05T17:13:28Z

Added a force fields section

@@ Line 9: / Line 9: @@
 ==Constraint algorithms==
 GROMACS can use either the [[SHAKE]] or the [[LINCS]] algorithms <ref>[http://www.gromacs.org/@api/deki/files/82/=gromacs4_manual.pdf GROMACS 4 Manual] &sect; 3.6 </ref>.
 ==References==
 <references/>

Carl McBride at 13:45, 9 February 2011

2011-02-09T13:45:10Z

← Older revision		Revision as of 15:45, 9 February 2011
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	<ref>[http://dx.doi.org/10.1002/jcc.20291 David Van Der Spoel, Erik Lindahl, Berk Hess, Gerrit Groenhof, Alan E. Mark, Herman J. C. Berendsen "GROMACS: Fast, flexible, and free", Journal of Computational Chemistry '''26''' pp. 1701-1718 (2005)]</ref>		<ref>[http://dx.doi.org/10.1002/jcc.20291 David Van Der Spoel, Erik Lindahl, Berk Hess, Gerrit Groenhof, Alan E. Mark, Herman J. C. Berendsen "GROMACS: Fast, flexible, and free", Journal of Computational Chemistry '''26''' pp. 1701-1718 (2005)]</ref>
	<ref>[http://dx.doi.org/10.1021/ct700301q Berk Hess, Carsten Kutzner, David van der Spoel and Erik Lindahl "GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation", Journal of Chemical Theory and Computation '''4''' pp. 435–447 (2008)]</ref>		<ref>[http://dx.doi.org/10.1021/ct700301q Berk Hess, Carsten Kutzner, David van der Spoel and Erik Lindahl "GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation", Journal of Chemical Theory and Computation '''4''' pp. 435–447 (2008)]</ref>
	is a versatile package to perform [[molecular dynamics]], i.e. simulate the		('''GRO'''ningen '''MA'''chine for '''C'''hemical '''S'''imulations) is a versatile package to perform [[molecular dynamics]], i.e. simulate the
	[[Newtons laws \|Newtonian equations of motion]] for systems with hundreds to millions of particles.		[[Newtons laws \|Newtonian equations of motion]] for systems with hundreds to millions of particles.
	GROMACS is primarily designed for [[Biological systems \|biochemical molecules]] like [[proteins]] and [[lipids]] that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the non-bonded interactions (that usually dominate simulations) many groups are also using it for research on non-biological systems, e.g. [[polymers]].		GROMACS is primarily designed for [[Biological systems \|biochemical molecules]] like [[proteins]] and [[lipids]] that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the non-bonded interactions (that usually dominate simulations) many groups are also using it for research on non-biological systems, e.g. [[polymers]].

Carl McBride: Added a note on the Constraint algorithms

2010-07-27T12:28:31Z

Added a note on the Constraint algorithms

← Older revision		Revision as of 14:28, 27 July 2010
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	==GROMACS on Tesla GPUs==		==GROMACS on Tesla GPUs==
	The CUDA port of GROMACS enabling GPU acceleration is now available in beta and supports [[Ewald sum#Particle mesh\|Particle-Mesh-Ewald]], arbitrary forms of non-bonded interactions, and implicit solvent Generalized Born methods <ref> source: [http://www.nvidia.com/object/gromacs_on_tesla.html NVIDIA]</ref>		The CUDA port of GROMACS enabling GPU acceleration is now available in beta and supports [[Ewald sum#Particle mesh\|Particle-Mesh-Ewald]], arbitrary forms of non-bonded interactions, and implicit solvent Generalized Born methods <ref> source: [http://www.nvidia.com/object/gromacs_on_tesla.html NVIDIA]</ref>
			==Constraint algorithms==
			GROMACS can use either the [[SHAKE]] or the [[LINCS]] algorithms <ref>[http://www.gromacs.org/@api/deki/files/82/=gromacs4_manual.pdf GROMACS 4 Manual] § 3.6 </ref>.
	==References==		==References==
	<references/>		<references/>

Carl McBride: Added GROMACS on Tesla GPUs section

2010-05-10T14:17:47Z

Added GROMACS on Tesla GPUs section

← Older revision		Revision as of 16:17, 10 May 2010
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	'''GROMACS''' is a versatile package to perform [[molecular dynamics]], i.e. simulate the		'''GROMACS''' <ref>[http://dx.doi.org/10.1016/0010-4655(95)00042-E H. J. C. Berendsen, D. van der Spoel and R. van Drunen "GROMACS: A message-passing parallel molecular dynamics implementation", Computer Physics Communications '''91''' pp. 43-56 (1995)]</ref>
			<ref>[http://dx.doi.org/10.1002/jcc.20291 David Van Der Spoel, Erik Lindahl, Berk Hess, Gerrit Groenhof, Alan E. Mark, Herman J. C. Berendsen "GROMACS: Fast, flexible, and free", Journal of Computational Chemistry '''26''' pp. 1701-1718 (2005)]</ref>
			<ref>[http://dx.doi.org/10.1021/ct700301q Berk Hess, Carsten Kutzner, David van der Spoel and Erik Lindahl "GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation", Journal of Chemical Theory and Computation '''4''' pp. 435–447 (2008)]</ref>
			is a versatile package to perform [[molecular dynamics]], i.e. simulate the
	[[Newtons laws \|Newtonian equations of motion]] for systems with hundreds to millions of particles.		[[Newtons laws \|Newtonian equations of motion]] for systems with hundreds to millions of particles.
	GROMACS is primarily designed for [[Biological systems \|biochemical molecules]] like [[proteins]] and [[lipids]] that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the non-bonded interactions (that usually dominate simulations) many groups are also using it for research on non-biological systems, e.g. [[polymers]].		GROMACS is primarily designed for [[Biological systems \|biochemical molecules]] like [[proteins]] and [[lipids]] that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the non-bonded interactions (that usually dominate simulations) many groups are also using it for research on non-biological systems, e.g. [[polymers]].
			==GROMACS on Tesla GPUs==
			The CUDA port of GROMACS enabling GPU acceleration is now available in beta and supports [[Ewald sum#Particle mesh\|Particle-Mesh-Ewald]], arbitrary forms of non-bonded interactions, and implicit solvent Generalized Born methods <ref> source: [http://www.nvidia.com/object/gromacs_on_tesla.html NVIDIA]</ref>
	==References==		==References==
	*[http://dx.doi.org/10.1016/0010-4655(95)00042-E H. J. C. Berendsen, D. van der Spoel and R. van Drunen "GROMACS: A message-passing parallel molecular dynamics implementation", Computer Physics Communications '''91''' pp. 43-56 (1995)]		<references/>
	*[http://dx.doi.org/10.1002/jcc.20291 David Van Der Spoel, Erik Lindahl, Berk Hess, Gerrit Groenhof, Alan E. Mark, Herman J. C. Berendsen "GROMACS: Fast, flexible, and free", Journal of Computational Chemistry '''26''' pp. 1701-1718 (2005)]
	*[http://dx.doi.org/10.1021/ct700301q Berk Hess, Carsten Kutzner, David van der Spoel and Erik Lindahl "GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation", Journal of Chemical Theory and Computation '''4''' pp. 435–447 (2008)]
	==External links==		==External links==
	*[http://www.gromacs.org/ GROMACS home page]		*[http://www.gromacs.org/ GROMACS home page]
	[[Category: Materials modelling and computer simulation codes]]		[[Category: Materials modelling and computer simulation codes]]

Carl McBride: Slight tidy.

2010-02-24T17:33:00Z

Slight tidy.

← Older revision		Revision as of 19:33, 24 February 2010
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	~~[http://www.gromacs.org/~~ GROMACS] is a versatile package to perform [[molecular dynamics]], i.e. simulate the		'''GROMACS''' is a versatile package to perform [[molecular dynamics]], i.e. simulate the
	[[Newtons laws \|Newtonian equations of motion]] for systems with hundreds to millions of particles.		[[Newtons laws \|Newtonian equations of motion]] for systems with hundreds to millions of particles.
			GROMACS is primarily designed for [[Biological systems \|biochemical molecules]] like [[proteins]] and [[lipids]] that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the non-bonded interactions (that usually dominate simulations) many groups are also using it for research on non-biological systems, e.g. [[polymers]].
	GROMACS is primarily designed for biochemical molecules like [[proteins]] and [[lipids]] that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the ~~nonbonded~~ interactions (that usually dominate simulations) many groups are also using it for research on non-biological systems, e.g. [[polymers]].

	~~Further information can be found in the wiki dedicated to GROMACS: [http://wiki.gromacs.org/ wiki.gromacs.org~~].
	==References==		==References==
	#[http://dx.doi.org/10.1016/0010-4655(95)00042-E H. J. C. Berendsen, D. van der Spoel and R. van Drunen "GROMACS: A message-passing parallel molecular dynamics implementation", Computer Physics Communications '''91''' pp. 43-56 (1995)]		*[http://dx.doi.org/10.1016/0010-4655(95)00042-E H. J. C. Berendsen, D. van der Spoel and R. van Drunen "GROMACS: A message-passing parallel molecular dynamics implementation", Computer Physics Communications '''91''' pp. 43-56 (1995)]
	#[http://dx.doi.org/10.1002/jcc.20291 David Van Der Spoel, Erik Lindahl, Berk Hess, Gerrit Groenhof, Alan E. Mark, Herman J. C. Berendsen "GROMACS: Fast, flexible, and free", Journal of Computational Chemistry '''26''' pp. 1701-1718 (2005)]		*[http://dx.doi.org/10.1002/jcc.20291 David Van Der Spoel, Erik Lindahl, Berk Hess, Gerrit Groenhof, Alan E. Mark, Herman J. C. Berendsen "GROMACS: Fast, flexible, and free", Journal of Computational Chemistry '''26''' pp. 1701-1718 (2005)]
	#[http://dx.doi.org/10.1021/ct700301q Berk Hess, Carsten Kutzner, David van der Spoel and Erik Lindahl "GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation", Journal of Chemical Theory and Computation '''4''' pp. 435–447 (2008)]		*[http://dx.doi.org/10.1021/ct700301q Berk Hess, Carsten Kutzner, David van der Spoel and Erik Lindahl "GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation", Journal of Chemical Theory and Computation '''4''' pp. 435–447 (2008)]
			==External links==
			*[http://www.gromacs.org/ GROMACS home page]
	[[Category: Materials modelling and computer simulation codes]]		[[Category: Materials modelling and computer simulation codes]]

Carl McBride: /* References */ Added a reference.

2009-05-05T10:05:21Z

References: Added a reference.

← Older revision		Revision as of 12:05, 5 May 2009
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	#[http://dx.doi.org/10.1016/0010-4655(95)00042-E H. J. C. Berendsen, D. van der Spoel and R. van Drunen "GROMACS: A message-passing parallel molecular dynamics implementation", Computer Physics Communications '''91''' pp. 43-56 (1995)]		#[http://dx.doi.org/10.1016/0010-4655(95)00042-E H. J. C. Berendsen, D. van der Spoel and R. van Drunen "GROMACS: A message-passing parallel molecular dynamics implementation", Computer Physics Communications '''91''' pp. 43-56 (1995)]
	#[http://dx.doi.org/10.1002/jcc.20291 David Van Der Spoel, Erik Lindahl, Berk Hess, Gerrit Groenhof, Alan E. Mark, Herman J. C. Berendsen "GROMACS: Fast, flexible, and free", Journal of Computational Chemistry '''26''' pp. 1701-1718 (2005)]		#[http://dx.doi.org/10.1002/jcc.20291 David Van Der Spoel, Erik Lindahl, Berk Hess, Gerrit Groenhof, Alan E. Mark, Herman J. C. Berendsen "GROMACS: Fast, flexible, and free", Journal of Computational Chemistry '''26''' pp. 1701-1718 (2005)]
			#[http://dx.doi.org/10.1021/ct700301q Berk Hess, Carsten Kutzner, David van der Spoel and Erik Lindahl "GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation", Journal of Chemical Theory and Computation '''4''' pp. 435–447 (2008)]
	[[Category: Materials modelling and computer simulation codes]]		[[Category: Materials modelling and computer simulation codes]]

Nice and Tidy at 17:56, 30 October 2007

2007-10-30T17:56:28Z

← Older revision		Revision as of 19:56, 30 October 2007
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	#[http://dx.doi.org/10.1016/0010-4655(95)00042-E H. J. C. Berendsen, D. van der Spoel and R. van Drunen "GROMACS: A message-passing parallel molecular dynamics implementation", Computer Physics Communications '''91''' pp. 43-56 (1995)]		#[http://dx.doi.org/10.1016/0010-4655(95)00042-E H. J. C. Berendsen, D. van der Spoel and R. van Drunen "GROMACS: A message-passing parallel molecular dynamics implementation", Computer Physics Communications '''91''' pp. 43-56 (1995)]
	#[http://dx.doi.org/10.1002/jcc.20291 David Van Der Spoel, Erik Lindahl, Berk Hess, Gerrit Groenhof, Alan E. Mark, Herman J. C. Berendsen "GROMACS: Fast, flexible, and free", Journal of Computational Chemistry '''26''' pp. 1701-1718 (2005)]		#[http://dx.doi.org/10.1002/jcc.20291 David Van Der Spoel, Erik Lindahl, Berk Hess, Gerrit Groenhof, Alan E. Mark, Herman J. C. Berendsen "GROMACS: Fast, flexible, and free", Journal of Computational Chemistry '''26''' pp. 1701-1718 (2005)]
	[[Category: Materials modelling and ~~Computer~~ simulation codes]]		[[Category: Materials modelling and computer simulation codes]]