
	Where results make sense

Topic: GROMACS

Related Topics

NAMD

Rapira

Molecular dynamics

Plural of virus

Acetylene

Tennessee Technological University

California State University, San Marcos

Animorphs

Morning

Ramjet

Boolean satisfiability problem

Roitika

Spice

France 3

Gibson (disambiguation)

	GROMACS - Wikipedia, the free encyclopedia
		GROMACS (Groningen Machine for Chemical Simulations) is a molecular dynamics simulation package developed in the University of Groningen.
		The GROMACS project was originally started to construct a dedicated parallel computer system for molecular simulations, based on a ring architecture.
		A notable use of GROMACS is in the distributed computing project Folding@home where it is used extensively in the simulation of protein folding.
	en.wikipedia.org /wiki/GROMACS (270 words)

	Gromacs
		GROMACS (www.gromacs.org) is a versatile package to perform molecular dynamics, i.e.
		Gromacs is available on both the SGI systems (Helix, Nimbus, Quasar) and on the
		In general, Gromacs is faster on the p1400 Biowulf nodes because of their faster cpu speeds, but does not scale as well as on the SGIs.
	helix.nih.gov /apps/structbio/gromacs.html (354 words)

	NSC: Chemistry: Gromacs
		Gromacs is a versatile package to perform molecular dynamics, i.e.
		The Gromacs 3.2 program is available to users at NSC under the condition that published work include citation of the program (see below).
		The Gromacs binaries are thereby to be located in your path.
	www.nsc.liu.se /software/chemistry/gromacs (309 words)

	MD Simulations of Villin Headpiece Subdomain (1VII) in Water
		In Gromacs, the periodic cell is built using the "editconf" command.
		In Gromacs energy minimization is performed using the "mdrun" command, with parameters specified by the "grompp" command (using an MDP file).
		To perform restrained MD in Gromacs, one executes the "grompp" command to setup the parameters (with an MDP file) followed by the "mdrun" command to run the dynamics.
	femto.cs.uiuc.edu /~sbond/reports/villin (1439 words)

	LRZ: GROMACS - A Molecular Dynamics Package
		GROMACS is licensed and redistributed under the GPL.
		GROMACS was first developed in Herman Berendsens group, department of Biophysical Chemistry of Groningen University.
		The Gromacs benchmark results for the LRZ HPC systems are also available.
	www.lrz-muenchen.de /services/software/chemie/gromacs (909 words)

	ATN Bioscience Computing - Application: Gromacs/Leap (Site not responding. Last check: 2007-10-13)
		Gromacs modules can be accessed with a SGI Desktop (IRIX 6.5) with an AFS Client installed.
		The PATH to access Gromacs modules and all necessary environment variables are set up properly.
		A line "gromacs" is shown which indicated that the environment for Gromacs is already set.
	www.unc.edu /atn/asg/applications/gromacs/gromacs/setup_unix.html (237 words)

	HPCx - GROMACS
		GROMACS is a versatile package for performing molecular dynamics calculations, i.e.
		GROMACS is primarily designed for biochemical molecules like proteins and lipids that have a large number of complicated bonded interactions.
		GROMACS can also be used for non-biological systems, e.g.
	www.hpcx.ac.uk /research/biochemistry/gromacs.html (114 words)

	Welcome to GROMACS (Site not responding. Last check: 2007-10-13)
		GROMACS supports all the usual algorithms you expect from a modern molecular dynamics implementation, (check the online reference or manual for details), but there are also quite a few features that make it stand out from the competition:
		GROMACS is user-friendly, with topologies and parameter files written in clear text format.
		GROMACS contains several state-of-the-art algorithms that make it possible to extend the time steps is simulations significantly, and thereby further enhance performance without sacrificing accuracy or detail.
	www.gromacs.org /features/index.php (621 words)

	AMDReview Forums - powerful folding rig (Site not responding. Last check: 2007-10-13)
		Gromacs should run 3 to 4 times as fast as tinkers on a P4.
		Gromacs should be all you use on a P4 because they are slow on tinkers.
		You must run forceasm with gromacs because if the client gets shut down just once incorrectly the optimizations are turned off.
	www.athlonxp.com /forums/showthread.php?s=32789d08709eaac6b18bef44ebaafc02&threadid=11208 (991 words)

	PRESS RELEASE GROMACS Molecular Dynamics Software Ported to ClearSpeed's Processor (Site not responding. Last check: 2007-10-13)
		GROMACS (www.gromacs.org) is an open-source application able to simulate the Newtonian equations of motion for systems made up of hundreds of millions of particles.
		It is primarily designed for biochemical molecules such as proteins and lipids that contain a high number of complicated bonded interactions.
		GROMACS is a broadly used tool in biological and medical research and the biopharmaceutical industry, and has additional use for non-biological molecular dynamics applications.
	www.marketwire.com /mw/release_html_b1?release_id=71777 (560 words)

	Folding@Home with Gromacs (Site not responding. Last check: 2007-10-13)
		For some calculations, gromacs affords benefits over the current code in Folding@Home (the current code is based on Jay Ponder's Tinker), especially a great speed increase (perhaps up to 10x-20x).
		In addition to the original Gromacs core (core 78), there are two additional Gromacs cores: The DGromacs core (core 79) is compiled for double precision calculations, for cases where higher precision is needed.
		The GBGromacs core (core 7A) adds the Generalized Born implicit solvent to Gromacs; we have set this up as a separate core since this technology is still a bit experimental and we do not want to taint the main production Gromacs core (core 78).
	folding.stanford.edu /gromacs.html (975 words)

	ABCC - Advanced Biomedical Computing Center
		GROMACS is a versatile modeling software developed to carry out molecular dynamics (MD) simulations for a wide-range of systems such as proteins, lipids and polymers.
		GROMACS has also the capability to run in parallel, and is a free software available under the GNU General Public license.
		The developers of GROMACS claim that their software is the fastest molecular dynamics (MD) program available.
	www.abcc.ncifcrf.gov /news/gromacs.shtml (126 words)

	Gromacs will be back soon - XtremeSystems Forums (Site not responding. Last check: 2007-10-13)
		I just read in the FAH forums that proteins using the Gromac core will be back in circulation within the week.
		The Gromac proteins run on, what else, the gromac core which is core_78.
		Stanford stopped handing out gromacs some time ago to work on some problems with the core, after receiving feedback from users.
	www.xtremesystems.org /forums/showthread.php?p=36929 (565 words)

	Xtreme Resources Forum - Time to do a Work Unit... Gromacs... a few questions ;) (Site not responding. Last check: 2007-10-13)
		If the WU's are available and you're a member of the beta team and are running with the correct client and command-line flags, your client will download a new core (fahcore_78.exe) and run the new work units.
		A few weeks ago when the project 997 and 998 work units were around (gromacs) my folding output doubled to more than 200 points per day.
		Gromacs are for the beta team for testing purposes before they're released to the public.
	www.xtremeresources.com /forums/showthread.php?t=7623 (725 words)

	Folding-community.org :: View topic - GROMACS power & temperature (Site not responding. Last check: 2007-10-13)
		There have been suggestions that GROMACS is causing higher CPU temperatures that result in numerical errors in some computers.
		The CPU temperature elevation in switching from core_65 to core_78 (GROMACS) seems to be roughly 1 or 1.5 deg C, and the power elevation about 7 Watts per CPU.
		Gromacs is one of the most optimized codes I've ever seen (that's why we're including it in F@H).
	forum.folding-community.org /viewtopic.php?t=1474 (1791 words)

	GROMACS
		GROMACS is Free Software, available under the GNU General Public License.
		Lindahl and B. Hess and D. van der Spoel: GROMACS 3.0: A package for molecular simulation and trajectory analysis.
		Note that GROMACS uses the term "node" where we use the term "processor".
	www.hlrn.de /doc/gromacs (439 words)

	IBM - Gromacs
		It 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 non-bonded interactions (that usually dominate simulations) many groups are also using it for research on non-biological systems, e.g.
		GROMACS supports all the usual algorithms you expect from a modern molecular dynamics implementation (check out http://www.gromacs.org for details), but it provides extremely high performance compared to all other programs.
		Gromacs is distributed as Free Software, licensed under the GPL.
	www-304.ibm.com /jct09002c/gsdod/solutiondetails.do?solution=13503&expand=true&lc=en (588 words)

	HHMI Research Journal 2003
		The plain installs of gromacs and fftw should be good to go on bazaar and cairo.
		The ring structure of GROMACS parallelization using MPI is slowly and reluctantly revealing its details.
		Determined that GROMACS is using ring structure in its usage of MPI.
	www.cs.earlham.edu /~mccoyjo/hhmi/log.html (980 words)

	GROMACS FAQ
		The details are available in the license text, but in short you can modify and redistribute the code as long as your version is licensed under the GPL too.
		This will hopefully be fixed in a future release of automake (it is not caused by Gromacs), but in the meantime you can install bash (if you don't already have it) and use the command '/bin/bash./configure' (Your bash location might be different from /bin/bash).
		If you compiled GROMACS with assembly loops there will be a line in the logfile telling you which loops we are using.
	www.esi.umontreal.ca /gromacs/gmxfaq.html (4254 words)

	Folding@Home AMBER ports for GROMACS (Site not responding. Last check: 2007-10-13)
		Additionally, improper torsions are handled in GROMACS using the proper dihedral definition to match the AMBER standard, rather than the default analytical function used for improper dihedrals in GROMACS.
		Information on using GROMACS as well as FAQs, tutorials, and a user forum are available at www.GROMACS.org.
		Also note that because GROMACS supports SOL=HOH water definitions, importing a solvated PDB with names other than HOH or SOL may cause the solvent molecules to be treated as part of the biopolymer rather than listing SOL molecules at the end of the topology, which has to be modified by hand after the fact.
	folding.stanford.edu /ffamber (2157 words)

	Gromacs slow. - Short-Media Forums
		Before Stanford reworked the points on Tinker work, the Gromacs work was the best units to get for points production but when Stanford switched benchmark machines to the P4 2.8 from the Celeron 500, the Tinker points worth went up a whole bunch.
		There's no real way to specify only Gromacs or only Tinker work, unfortunately, and I wish there was so I could keep the Tinkers off my P4 rigs.
		Gromacs do like 3x more work, as in data calculations, than tinkers do.
	www.short-media.com /forum/showthread.php?t=17896 (756 words)

	Advanced Biomedical Computing Center:Gromacs infomation
		For more detailed information on how to use GROMACS, read the on-line manual available at http://gromacs.org/documentation/ Plesae cite these articles when you publish research using GROMACS: 1) Berendsen, H.J.C., van der Spoel, D. and van Drunen, R., GROMACS: A message-passing parallel molecular dynamics implementation, Comp.
		2) Lindahl, E., Hess, B. and van der Spoel, D., GROMACS 3.0: A package for molecular simulation and trajectory analysis J. Mol.
		GROMACS Demo: ------------- GROMACS demo is run using a C-Shell script.
	www.abcc.ncifcrf.gov /app/htdocs/appdb/appinfo.php?appname=Gromacs (320 words)

	News
		We have been investigating the previous issues of certain types of Gromacs calculations on OSX and we believe that the the issues are now resolved.
		Gromacs was originally released as an advanced only WU until we could work things out to make it more stable.
		We are testing the Gromacs core for Win32 internally as well as a new version of the client which allows for a simple and direct way to choose projects (F@H vs G@H).
	www.stanford.edu /group/pandegroup/folding/news.html (10642 words)

	Water
		You are encouraged to look up the different programs and file formats in the online manual while you are browsing through the examples;underlined file formats or programs contain a link to the Gromacs manual.
		Gromacs has a lot of specialized programs that allow you to calculate a wide variety of properties of your system.
		The second, third line and fourth line (respectively "a OW", "a H*" and "q") is what you are supposed to type to the input line of the program make_ndx.
	www.nmr.chem.uu.nl /ccc/water.html (1900 words)

	Interactive Essential Dynamics
		In general, GROMACS is preferred for working with GROMACS format trajectories, and ptraj is preferred for working with AMBER or CHARMM format trajectories.
		When using GROMACS to prepare input for IED, one uses g_covar to find the eigenvectors and then g_anaeig to generate the projections of the trajectory onto the eigenvectors.
		There is one problem with using GROMACS to analyze AMBER data: GROMACS assumes coordinates are in nanometers, while AMBER writes them in Angstroms.You can ignore this problem, in which case all your atoms will be ten times further apart than they should be in IED.
	mccammon.ucsd.edu /ied (1993 words)

	GRIDtoday: GROMACS BIOCHEMICAL SOFTWARE PORTED TO ClearSpeed PROCESSOR
		ClearSpeed Technology, developer of high performance, low power, programmable microprocessor solutions, announced that some of the most computationally-intensive inner loops of GROMACS, a molecular dynamics software application, are now ported and off-loaded to ClearSpeed's PCI plug-in accelerator card.
		GROMACS is an open-source application able to simulate the Newtonian equations of motion for systems made up of hundreds of millions of particles.
		Folding@home (folding.stanford.edu) uses GROMACS as its main compute engine.
	www.gridtoday.com /04/0830/103718.html (421 words)

	Cores - FaHWiki
		Gromacs (Groningen Machine for Chemical Simulations) is a single-precision scientific core that is used for the majority of F@H calculations.
		It is developed by the University of Groningen under the GPL and is writen in Fortran77-based GROMOS in C. Gromacs takes advantage of SIMD, including SSE and AltiVec instructions in processors equipped with them to provide a nearly 3x increase in calculation speed.
		The Gromacs 33 core contains features from more recent versions of Gromacs ported to Folding @Home, allowing a broader range of simulations to be run.
	fahwiki.net /index.php/Cores (489 words)

	Josh Hursey's Cluster Research Log File
		I have been tracing the MPI usage in GROMACS, and wrote up a useful reference for network.c which is Here.
		The bug with the GROMACS Altivec Assembly, was that when one uses the -O3 gcc compiler optimizations it fails, but with -O0 it works.
		Started to look at ways to move Gromacs to MP_Lite, but tabled it until I have a large chunk of time to dedicate to it.
	cluster.earlham.edu /~joshh/doc/log/log.html (3525 words)

	GROMACS (Site not responding. Last check: 2007-10-13)
		GROMACS (Groningen Machine for Chemical Simulations) is a versatile package to perform molecular dynamics, i.e.
		GROMACS calling structure is quite complicated, and it is not recommended that users proceed without at least becoming familiar with the program.
		The examples should be considered a guide and not a definitive step-by-step instruction set.
	www.psc.edu /general/software/packages/gromacs (233 words)

	GROMACS Frequently Answered Questions (Site not responding. Last check: 2007-10-13)
		Since this FAQ is written for version 2.0, not all of the solutions may apply to previous GROMACS versions.
		For all these systems GROMACS normally compiles without any problems, and can also run in parallel (providing a good version of MPI or PVM is present).
		Due to the fact that we initially developed GROMACS to run on our home-built parallel machine, with only 8Mb of memory per processor, the code is quite well optimized for memory use.
	www.cnslab.carleton.ca /gromacs/faq (3020 words)

Try your search on: Qwika (all wikis)