Category: GROMACS

Gromacs manual grompp

#725013 – gromacs-openmpi: grompp crashes with invalid GROMACS Molecular Dynamics & GPU Acceleration | NVIDIA Instead, frustrated and confused. The man was slumped over, but he absorbed the blow and stumbled back. But I think it will be better used in this situation.He stopped at my open window to address…

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GROMACS with Erik Lindahl

Speaker: Erik Lindahl, Stockholm University & Royal Institute of Technology GROMACS is a state-of-the-art computational tool to understand the molecular mechanisms of the protein molecules in our cells. Eric’s lab leads the development of the GROMACS molecular dynamics toolkit, which is one of the world’s most widely used HPC applications….

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gromacs-plumed | MacPorts

Molecular dynamics package designed for simulations of proteins, lipids, and nucleic acids.: (THIS PORT INSTALLS A VERSION OF GROMACS PATCHED WITH PLUMED) GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. It is primarily designed…

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Nose hoover lammps manual

Nose hoover lammps manual 科学网—[转载]谈谈分子模拟中的能量最小化,弛豫和平衡态 – 周龙 …NVT run with LAMMPS | Tools and tricks for computational A serious man with a comic face-walrus mustache, had long ago wanted to tear the old girl down and replace her with a gleaming…

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gmx_wallcycle.h | searchcode

gmx_wallcycle.h | searchcode PageRenderTime 23ms CodeModel.GetById 14ms app.highlight 6ms RepoModel.GetById 1ms app.codeStats 0ms /pdalcin-Gromacs-GA-458371f/gromacs-4.0.7/include/gmx_wallcycle.h github.com/pdalcin/Gromacs_GA C++ Header…

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435.gromacs: SPEC CPU2006 Benchmark Description

435.gromacs: SPEC CPU2006 Benchmark Description Benchmark Name 435.gromacs Benchmark Author Erik Lindahl <lindahl [at] gromacs.org>Department of Structural BiologyStockholm Bioinformatics CentreStockholmSweden David van der Spoel <spoel [at] gromacs.org>Department of BiochemistryUppsala UniversityBox 576, 751 23 UppsalaSWEDEN Benchmark Program General Category Chemistry / Molecular Dynamics Benchmark Description 435.gromacs is derived from GROMACS, a…

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File input/output error gromacs

File input/output error gromacs 13-10-2021 If an option takes multiple arguments (such as the multi-file input -f. file For more information and tips for troubleshooting, as it will tell you error one is missing? file…

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ExceptionInfo Class Template Reference

template<class Tag, typename T>class gmx::ExceptionInfo< Tag, T > Stores additional context information for exceptions. Template Parameters Tag Tag type (typically, a forward-declared struct that is not defined anywhere) that makes all ExceptionInfo types unique, even if they have the same value type. T Type of value this object stores. Needs…

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Gromacs: gmx::SimdDouble Class Reference

#include <gromacs/simd/impl_reference/impl_reference_simd_double.h> Double SIMD variable. Available if GMX_SIMD_HAVE_DOUBLE is 1. Note This variable cannot be placed inside other structures or classes, since some compilers (including at least clang-3.7) appear to lose the alignment. This is likely particularly severe when allocating such memory on the heap, but it occurs for stack…

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Gromacs: gmx::ImdSession::Impl Class Reference

Implementation type for the IMD session. Todo: Make this class (or one extracted from it) model IForceProvider. Use RAII for files and allocations   Impl (const MDLogger &mdlog)   Constructor.   void  prepareMasterSocket ()   Prepare the socket on the MASTER.   void  disconnectClient ()   Disconnect the client.  …

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Gromacs: PmeGpuConstParams Struct Reference

#include <gromacs/ewald/pme_gpu_types.h> Description A GPU data structure for storing the constant PME data. This only has to be initialized once. Public Attributes float  elFactor   Electrostatics coefficient = ONE_4PI_EPS0 / pme->epsilon_r.   DeviceBuffer< float >  d_virialAndEnergy [2]   Virial and energy GPU array. Size is c_virialAndEnergyCount (7) floats. The element…

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Gromacs: gmx::BiasWriter Class Reference

#include <gromacs/applied_forces/awh/biaswriter.h> Description Class organizing the output data storing and writing of an AWH bias. Constructor & Destructor Documentation gmx::BiasWriter::BiasWriter ( const Bias &  bias ) Member Function Documentation int gmx::BiasWriter::numBlocks ( ) const inline Returns the number of data blocks. Returns the number of data blocks. int gmx::BiasWriter::writeToEnergySubblocks (…

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Maximizing GROMACS Throughput with Multiple Simulations per GPU Using MPS and MIG

GROMACS, a simulation package for biomolecular systems, is one of the most highly used scientific software applications worldwide, and a key tool in understanding important biological processes including those underlying the current COVID-19 pandemic. In a previous post, we showcased recent optimizations, performed in collaboration with the core development team,…

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Barostat cp2k error

Barostat cp2k error 08-10-2021 right! like your idea. suggest error barostat cp2k attentively would read, but has CP2K or with plane-wave-based codes such as Error. Espresso. In doing so, the Rahman barostat The statistical…

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Research data supporting ‘Physics-driven coarse-grained model for biomolecular phase separation with near-quantitative accuracy’

Citation Joseph, J., Reinhardt, A., Aguirre, A., Chew, P. Y., Russell, K., Rene Espinosa, J., Garaizar, A., & et al. (2021). Research data supporting ‘Physics-driven coarse-grained model for biomolecular phase separation with near-quantitative accuracy’ [Dataset]. www.repository.cam.ac.uk/handle/1810/329039 Description This file is part of the supporting data for the manuscript ‘Physics-driven coarse-grained…

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Gromacs Solvant Box : Biochemistry

Hi Gromacs Alogrithm help. What I have: We have unit water boxes spc, tp etc. They have opposite sides complementary to each other (please correct me) such that if stacked together we get a uniform water box. “solvate” method creates a bigger box from unit boxes. What I did I…

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Gromacs: MoleculeBlockIndices Struct Reference

#include <gromacs/topology/topology.h> Indices for a gmx_molblock_t, derived from other gmx_mtop_t contents. int  numAtomsPerMolecule   Number of atoms in a molecule in the block.   int  globalAtomStart   Global atom index of the first atom in the block.   int  globalAtomEnd   Global atom index + 1 of the last atom…

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Gromacs Solvent Box Extension

Gromacs Solvent Box Extension 0 Hi Gromacs Alogrithm help. What I have: Gromacs have unit water boxes spc, tp etc. They have opposite sides complementary to each other (please correct me) such that if stacked together we get a uniform water box. “solvate” method creates a bigger box from unit…

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Gromacs: src/gromacs/gpu_utils/ocl_caching.cpp File Reference

Functions std::string  gmx::ocl::makeBinaryCacheFilename (const std::string &kernelFilename, cl_device_id deviceId)   Construct the name for the binary cache file. More…   cl_program  gmx::ocl::makeProgramFromCache (const std::string &filename, cl_context context, cl_device_id deviceId)   Check if there’s a valid cache available, and return it if so. More…   void  gmx::ocl::writeBinaryToCache (cl_program program, const std::string &filename)…

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Gromacs: gmx::OptionsIterator Class Reference

Decorator class for visiting options in a Options object. This class provides an interface for looping through sections and options in a Options object. Typical use (loop over all options, iteratively descending into subsections): { public: virtual void visitSection(const OptionSectionInfo &section) { iterator.acceptSections(this); iterator.acceptOptions(this); } virtual void visitOption(const OptionInfo &option)…

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Gromacs: src/gromacs/coordinateio/tests/outputadapters.h File Reference

Classes class   gmx::test::SetAtomsSupportedFiles   Helper to test supported file names. More…   class   gmx::test::SetAtomsUnSupportedFiles   Helper to test supported file names. More…   class   gmx::test::AnyOutputSupportedFiles   Helper to test supported file names. More…   class   gmx::test::NoOptionalOutput   Helper to test support for disabling all output options….

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gromacs-2021.3.tar.gz: …/src/compression/dict.c | Fossies

gromacs-2021.3.tar.gz: …/src/compression/dict.c | Fossies “Fossies” – the Fresh Open Source Software Archive Member “gromacs-2021.3/src/external/tng_io/src/compression/dict.c” (18 Aug 2021, 972 Bytes) of package /linux/privat/gromacs-2021.3.tar.gz: As a special service “Fossies” has tried to format the requested source page into HTML format using (guessed) C and C++ source code syntax highlighting (style: standard) with…

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GROMACS: …/DensitySimilarityTest_CrossCorrelationGradientIsCorrect.xml | Fossies

GROMACS: …/DensitySimilarityTest_CrossCorrelationGradientIsCorrect.xml | Fossies “Fossies” – the Fresh Open Source Software Archive Member “gromacs-2021.3/src/gromacs/math/tests/refdata/DensitySimilarityTest_CrossCorrelationGradientIsCorrect.xml” (18 Aug 2021, 1050 Bytes) of package /linux/privat/gromacs-2021.3.tar.gz: As a special service “Fossies” has tried to format the requested source page into HTML format using (guessed) XML source code syntax highlighting (style: standard) with prefixed line…

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Gromacs: src/gromacs/topology Directory Reference

Directory dependency graph for topology: This browser is not able to show SVG: try Firefox, Chrome, Safari, or Opera instead. Directories directory   tests   Files file   atomprop.cpp   file   atomprop.h   file   atoms.cpp   file   atoms.h   file   atomsbuilder.cpp   Implements classes from atomsbuilder.h….

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GROMACS adopts hipSYCL for future AMD GPU support

It was attractive to consider using SYCL in GROMACS also for AMD GPUs, since there was already effort underway in GROMACS in that direction targeting Intel GPUs. The hipSYCL (github.com/illuhad/hipSYCL) open-source project run at Heidelberg University already supported CPUs, as well as Nvidia and AMD GPUs in SYCL  by extending…

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ananvodo

ananvodo/appmode 0 A Jupyter extensions that turns notebooks into web applications. ananvodo/Potential-of-Mean-Force 0 This is a program a plug-and-play program to create all files needed to calculate Potential of Mean Force in Gromacs (any gromacs version) ananvodo/python-quality-threshold 0 a python implementation of the quality threshold clustering algorithm of Heyer, 1999,…

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Gromacs mdp options 2019

Gromacs mdp options 2019 Revision History | Winmostar(TM)LATEST PERFORMANCE ENHANCEMENTS TO GROMACS ON …g_mmpbsa Mailing List – Google Groups I was ready to marry her on the first date, but I also have two classes this morning, pushing aside the fear…

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Gromacs Contact Map | Contact Information Finder

Listing Results Gromacs Contact Map Contact maps using Gromacs ResearchGate Just Now Researchgate.net View All Contact maps using Gromacs ? I used gmx mdmat in gromacs to create contact maps, but it seems that the mdmat gives the minimum average distance rather than the average centre-of-mass distance. Estimated Reading Time:…

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marked as done (gromacs build-depends on gcc-9)

Your message dated Sat, 18 Sep 2021 15:37:04 +0000 with message-id <e1mrcom-0000pb…@fasolo.debian.org> and subject line Bug#994290: fixed in gromacs 2021.3-3 has caused the Debian Bug report #994290, regarding gromacs build-depends on gcc-9 to be marked as done. This means that you claim that the problem has been dealt with. If…

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Gromacs: File Members

Gromacs  2018.4 Main Page Modules Other Docs Namespaces Classes Files Examples File List File Members All Functions Variables Typedefs Enumerations Enumerator Macros _ a b c d e f g h i k l m n o p r s t u v w z  All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Macros Groups Pages   – v – v_lj_ewald_lr() : forcetable.h v_q_ewald_lr()…

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Accepted gromacs 2021.3-3 (source) into unstable

—–BEGIN PGP SIGNED MESSAGE—– Hash: SHA256 Format: 1.8 Date: Sat, 18 Sep 2021 08:17:59 -0700 Source: gromacs Architecture: source Version: 2021.3-3 Distribution: unstable Urgency: medium Maintainer: Debichem Team <debichem-de…@lists.alioth.debian.org> Changed-By: Nicholas Breen <nbr…@debian.org> Closes: 994290 Changes: gromacs (2021.3-3) unstable; urgency=medium . * With GCC 10.3 in testing for all release…

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Gromacs: gmx::ISerializer Class Reference

#include <gromacs/utility/iserializer.h> Inherited by anonymous_namespace{keyvaluetreeserializer.cpp}::RefDataSerializer, gmx::FileIOXdrSerializer, gmx::InMemoryDeserializer, and gmx::InMemorySerializer. Interface for types that convert standard data types into a form suitable for storage or transfer. Different implementations could suit MPI, file I/O, or in-memory conversion. virtual bool  reading () const =0   Returns whether the serializer is reading or writing,…

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OpenClTraits Struct Template Reference

#include <gromacs/gpu_utils/oclraii.h> This browser is not able to show SVG: try Firefox, Chrome, Safari, or Opera instead. [legend] This browser is not able to show SVG: try Firefox, Chrome, Safari, or Opera instead. [legend] template<>struct gmx::OpenClTraits< cl_program > Implements traits for cl_program. using  ReleaserType = cl_int(*)(cl_program)   Type of the…

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Gromacs: Class Members – Variables

Gromacs: Class Members – Variables   – n – N : t_UmbrellaWindow , t_bb n : t_coordselection , t_methoddata_kwreal , t_methoddata_permute , t_partition , gmx_fft_fftpack , t_spheresurfacebin , t_methoddata_kwint n_alloc : t_spheresurfacebin n_at_lam : df_history_t n_dev : gmx_gpu_info_t n_dev_compatible : gmx_gpu_info_t nalloc : cu_atomdata , cl_atomdata , gmx_ana_selvalue_t , swap_compartment…

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python – python2.7.12 do not contain numpy also not pip so i cant run my program in gromacs

I manually download Python 2.7.12 because in my charm file the python2.7.15+ does not work. In my Python 2.7.12 there is no pip command, so I cant install networkx & numpy packages. What can I do to run python cgenff_charmm2gmx.py JZ4 jz4_fix.mol2 jz4.str charmm36-mar2019.ff I am trying to boostrap pip…

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Gromacs: gmx::ICheckpointHelperClient Class Reference

Client that needs to store data during checkpointing. Clients receive a CheckpointData object for reading and writing. Note that ReadCheckpointData is a typedef for CheckpointData<CheckpointDataOperation::Read>, and WriteCheckpointData is a typedef for CheckpointData<CheckpointDataOperation::Write>. This allows clients to write a single templated function, e.g. template<CheckpointDataOperation operation> void doCheckpointData(CheckpointData<operation>* checkpointData, const t_commrec* cr)…

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Tau t gromacs manual

Tau t gromacs manual TAU at TACC – TACC User PortalBiomolecules | Free Full-Text | Electrostatics of Tau GN Drive Tau | The Gundam Wiki | Fandom Kirk took a break and sent out for coffee when a patrolman brought him…

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Gromacs: gmx::KeyValueTreeTransformRulesScoped Class Reference

Public Member Functions   KeyValueTreeTransformRulesScoped (internal::KeyValueTreeTransformerImpl *impl, const KeyValueTreePath &prefix)   Internal constructor for creating the scope.     KeyValueTreeTransformRulesScoped (KeyValueTreeTransformRulesScoped &&other)   Supports returning the object from IKeyValueTreeTransformRules::scopedTransform().   KeyValueTreeTransformRulesScoped &  operator= (KeyValueTreeTransformRulesScoped &&other)   Supports returning the object from IKeyValueTreeTransformRules::scopedTransform().   IKeyValueTreeTransformRules *  rules ()   Returns the…

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Topology generation for non-standard molecules in GROMACS : comp_chem

I have just started working in the field of molecular dynamics and using gromacs for my studies. The problem that I am facing is topology generation for non-standard molecules. I looked into the gromacs manual on how to add residue to a forcefield but that is quite confusing. I started…

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Gromacs 4.5.4 manual

Gromacs 4.5.4 manual OntheStabilityofNegativelyChargedPlatelets inCalcium g_energy(1) [debian man page] Gromacs User Manual Version 4.6The defence of Königsberg had cost the lives of 42,000 German soldiers and 25,000 civilians. He yanked the seaman out and shouted at him to report straight to…

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Industry Trends, Growth, Size, Segmentation, Future Demands, Latest Innovation, Sales Revenue by Regional Forecast

The latest research report on Molecular Dynamics Software market meticulously explains the key factors influencing the industry performance over 2021-2026, so as to help stakeholders gain a competitive edge. Further, it validates the forecasts mentioned through statistical data and proven research methodologies. Besides, the document offers recommendations to assist firms…

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Gromacs: gmx_ffparams_t Struct Reference

#include <gromacs/topology/forcefieldparameters.h> Struct that holds all force field parameters for the simulated system. int  numTypes () const   Returns the number of function types, which matches the number of elements in iparams.   int  atnr = 0   The number of non-bonded atom types.   std::vector< t_functype >  functype  …

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Gromacs: src/gromacs/pbcutil/pbc.cpp File Reference

Implements routines in pbc.h. Utility functions for handling periodic boundary conditions. Mainly used in analysis tools. #define  BOX_MARGIN   1.0010   Margin factor for error message.   #define  BOX_MARGIN_CORRECT   1.0005   Margin correction if the box is too skewed.   enum   {   epbcdxRECTANGULAR = 1, epbcdxTRICLINIC, epbcdx2D_RECT, epbcdx2D_TRIC,   epbcdx1D_RECT, epbcdx1D_TRIC, epbcdxSCREW_RECT, epbcdxSCREW_TRIC,…

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Gromacs: gmx::AnalysisDataStorageFrame Class Reference

#include <gromacs/analysisdata/datastorage.h> Allows assigning values for a data frame in AnalysisDataStorage. This class implements the necessary methods to add new data into the storage. AnalysisDataStorage::startFrame() returns an object of this type, which can be used to add one or more point sets to that data frame. When all data has…

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Gromacs: Namespace Members

Here is a list of all documented namespace members with links to the namespaces they belong to: – d – decideWhetherToUseGpusForBonded() : gmx decideWhetherToUseGpusForNonbonded() : gmx decideWhetherToUseGpusForNonbondedWithThreadMpi() : gmx decideWhetherToUseGpusForPme() : gmx decideWhetherToUseGpusForPmeWithThreadMpi() : gmx DefaultRandomEngine : gmx detectGroup() : gmx Distribution : gmx do_lincs() : gmx do_lincsp() : gmx…

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Gromacs: gmx::LegacyInput Class Reference

#include <gromacs/mdrun/simulatorbuilder.h> Collaboration diagram for gmx::LegacyInput: This browser is not able to show SVG: try Firefox, Chrome, Safari, or Opera instead. [legend] Description Collection of legacy input information. Public Member Functions   LegacyInput (int filenamesSize, const t_filenm *filenamesData, t_inputrec *inputRec, t_forcerec *forceRec)   Build collection from legacy input data.  …

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Gromacs: gmx::Update Class Reference

#include <gromacs/mdlib/update.h> Description Contains data for update phase. Classes class   Impl   pImpled implementation for Update More…   Public Member Functions   Update (const t_inputrec *ir, BoxDeformation *boxDeformation)   Constructor.   gmx_stochd_t *  sd () const   Returns handle to stochd_t struct.   PaddedVector< gmx::RVec > *  xp ()…

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Http://manual.gromacs.org – vodosp.ru

Installation guide — GROMACS 2021.3 documentation 05 September 2021 – clk-950 steren manual citroen hy bedienungsanleitung manual treadmill deals bosch bsl 2470 battery charger manual bedienungsanleitung pfaff tipmatic 6120 bki handbuch kostenplanung im hochbau pdf lavarropas columbia lsc 10000 manual Molecular Simulations: Fundamentals and Practice wood manual recliner GROMACS COMMANDS…

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Gromacs: Member List

This is the complete list of members for gmx::Int64Option, including all inherited members. AbstractOption(const char *name) gmx::AbstractOption inlineexplicitprotected allowMultiple(bool bMulti=true) gmx::OptionTemplate< gmx_int64_t, Int64Option > inline clearFlag(OptionFlag flag) gmx::AbstractOption inlineprotected defaultValue(const gmx_int64_t &defaultValue) gmx::OptionTemplate< gmx_int64_t, Int64Option > inline defaultValue() const gmx::OptionTemplate< gmx_int64_t, Int64Option > inlineprotected defaultValueIfSet(const gmx_int64_t &defaultValue) gmx::OptionTemplate< gmx_int64_t, Int64Option…

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New and improved features — GROMACS 2020.3 documentation

  Density-guided simulations Users can now apply additional forces from three dimensional reference densities. These forces can be used to “fit” atoms into the densities by increasing the similarity of a simulated density to the reference density. Multiple protocols are available for how to calculate simulated densities as well as…

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Gromacs: src/gromacs/listed-forces/disre.h File Reference

Declares functions for handling distance restraints. void  init_disres (FILE *fplog, const gmx_mtop_t *mtop, t_inputrec *ir, const t_commrec *cr, t_fcdata *fcd, t_state *state, gmx_bool bIsREMD)   Initiates *fcd data. More…   void  calc_disres_R_6 (const t_commrec *cr, int nfa, const t_iatom *fa, const rvec *x, const t_pbc *pbc, t_fcdata *fcd, history_t *hist)…

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Gromacs: gmx::Int64Option Class Reference

Specifies an option that provides 64-bit integer values. Public methods in this class do not throw. See Also IntegerOption typedef OptionTemplate < gmx_int64_t, Int64Option >  MyBase   Alias for the template class for use in base classes.   const gmx_int64_t *  defaultValue () const   Returns a pointer to user-specified…

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Shell molecular dynamics — GROMACS 2020.4 documentation

  GROMACS can simulate polarizability using the shell model of Dick and Overhauser 43. In such models a shell particle representing the electronic degrees of freedom is attached to a nucleus by a spring. The potential energy is minimized with respect to the shell position at every step of the simulation…

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Gromacs: gmx::internal Namespace Reference

Internal GROMACS namespace. This namespace is used to contain some implementation-specific functions and classes. These are not meant for direct user access, but typically reside in public headers because of implementation reasons. template<typename T > static void  ignoreValueHelper (const T &)   Helper for ignoring values in macros. More…  …

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Debian — Details of package libgromacs5 in bullseye

GROMACS molecular dynamics sim, shared libraries GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. It is primarily designed for biochemical molecules like proteins and lipids that have a lot of complicated bonded interactions, but…

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Gromacs: src/gromacs/gmxlib Directory Reference

Directory dependency graph for gmxlib: This browser is not able to show SVG: try Firefox, Chrome, Safari, or Opera instead. Files file   calcgrid.c   file   chargegroup.c   file   checkpoint.cpp   file   conformation-utilities.c   file   conformation-utilities.h   file   copyrite.cpp   file   disre.c   file…

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Accepted gromacs 2021.3-2 (source) into unstable

—–BEGIN PGP SIGNED MESSAGE—– Hash: SHA256 Format: 1.8 Date: Fri, 20 Aug 2021 13:02:03 -0700 Source: gromacs Architecture: source Version: 2021.3-2 Distribution: unstable Urgency: medium Maintainer: Debichem Team <debichem-de…@lists.alioth.debian.org> Changed-By: Nicholas Breen <nbr…@debian.org> Changes: gromacs (2021.3-2) unstable; urgency=medium . * Switch to GCC 9 for mips*el, as GCC 11 is…

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Queries regarding temperature gradient

Post by Sabreen FarnazDear all,This is in regard to my previous queries. The warning in NVT step canpossibly be ignored using -maxwarn but I am still not sure about the rest!Can someone please help? tau_t = -1 means temperature coupling is not applied. Whether that’swhat you want or not is…

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GROMACS: src/gromacs/ewald/pme_pp.h | Fossies

GROMACS: src/gromacs/ewald/pme_pp.h | Fossies “Fossies” – the Fresh Open Source Software Archive Member “gromacs-2021.3/src/gromacs/ewald/pme_pp.h” (18 Aug 2021, 5141 Bytes) of package /linux/privat/gromacs-2021.3.tar.gz: As a special service “Fossies” has tried to format the requested source page into HTML format using (guessed) C and C++ source code syntax highlighting (style: standard) with…

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GROMACS: src/gromacs/utility/any.h | Fossies

GROMACS: src/gromacs/utility/any.h | Fossies “Fossies” – the Fresh Open Source Software Archive Member “gromacs-2021.3/src/gromacs/utility/any.h” (18 Aug 2021, 8080 Bytes) of package /linux/privat/gromacs-2021.3.tar.gz: As a special service “Fossies” has tried to format the requested source page into HTML format using (guessed) C and C++ source code syntax highlighting (style: standard) with…

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gromacs 2021.3 – Download, Browsing & More

“Fossies” – the Fresh Open Source Software Archive Contents of gromacs-2021.3.tar.gz (18 Aug 11:51, 37987972 Bytes) About: GROMACS performs molecular dynamics, i.e. simulates the Newtonian equations of motion for systems with hundreds to millions of particles (designed for biochemical molecules but used also for e.g. polymers). Release of 2020 series….

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Gromacs: gmx::AlignedAllocationPolicy Class Reference

#include <gromacs/utility/alignedallocator.h> Policy class for configuring gmx::Allocator, to manage allocations of aligned memory for SIMD code. static std::size_t  alignment ()   Return the alignment size.   static void *  malloc (std::size_t bytes)   Allocate memory aligned to alignment() bytes. More…   static void  free (void *p)   Free aligned memory….

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