Tag: GROMACS

Building Modified DNA topology – User discussions

GROMACS version: 2021.4GROMACS modification: Yes/NoHere post your question I am having trouble generating topology for a type of modified DNA, but I’m not sure how to do it.In fact, there is a 35-nucleotide sequence of ssDNA. Using the Discovery Studio program, I converted the Thymidine Oxygen 4 atom to Sulfur…

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gromacs 2021.5 – Download, Browsing & More

gromacs 2021.5 – Download, Browsing & More | Fossies Archive “Fossies” – the Fresh Open Source Software Archive Contents of gromacs-2021.5.tar.gz (14 Jan 16:58, 38023772 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…

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[gmx-users] grompp -check14

Post by Dongsheng ZhangDear all,Has anyone used -check14 for grompp? When I tried it just now, I gotsegmentation fault. grompp works fine without the option -check14 (orgrompp -f md01.mdp -c ala5 -p ala5 -check14 -o fullBack Off! I just backed up mdout.mdp to ./#mdout.mdp.1#checking input for internal consistency…calling /lib/cpp…processing topology…Generated…

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[gmx-users] Scaling in gromacs

Dear GMX users In order to benchmark my simulation system I would like to know in gromacswhich code scales linearly till 10K cores? ThanksBest RegardsPraveen—Thanks & RegardsDr. Praveen Kumar Sappidi,DST-National Postdoctoral FellowComputational Nanoscience LabChemical Engineering Department,IIT Kanpur —Gromacs Users mailing list * Please search the archive at www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!…

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[gmx-users] The grompp problem!! (Urgently)

I am doing the Drug-enzyme tutorial.I also generated the drg.itp, drg.gro files using PRODRG server.However, when I use the grompp command before the energy minimizationI face some error A fatal error was shown: atom types CR61 not found The atom type CR61 is presented in the drg.itp file that I…

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Comprehensive, hands-on tutorial for DNA-ligand MDS – User discussions

GROMACS version: 2021.4-HomebrewGROMACS modification: No Hello, guys. I am very new to molecular dynamics and I come from biomedical background. Recently, my boss asked me to gather additional data about interaction of a small molecule and an aberrant double-stranded DNA structure. I originally did docking experiments in Vina, and he…

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Bio/pharma vs. materials – can anyone speak of specializing in either of these? : comp_chem

It seems like most comp chemists lie on the spectrum in terms of their research application, which spreads from biochemical (proteins, drug design, biomolecular simulations, etc.) to inorganic materials (semiconductors, minerals/crystals, battery/electrolytes, alloys, metals, etc.). I think it’s a notable spectrum because these fields have entirely different software suites dedicated…

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runing a command multiple times in different nodes in SLURM

I want to run three instances of GROMACS mdrun on three different nodes. I have three temperatures 200,220 and 240 K and I want to run 200 K simulation on node 1, 220 K simulation on node 2 and 240 K simulation on node 3. I need to do all…

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[gmx-users] abnormal stop of job

In tis case it must have been your sysadmin or your queueing system. Check the other answers in this thread. Post by Samrat PalHi Elton,But I have neither killed the job nor I pressed Ctrl-C in the foreground.The job was practically running background.ThanksAtanu________________________________From: Elton Carvalho To: Discussion list for GROMACS…

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[gmx-users] Grompp Error No default Ryckaert-Bell. types

Dear gromacs users. I am simulating a molecule in opls-aa force field.While running energy minimization I did get the error“No default Ryckaert-Bell. types”. I checked the line in topol.top and it says that dihedral for ( C-CT-OH-HO)has No default Ryckaert-Bell. types. but on checking ffbonded.itp I foundthat this dihedral is…

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How to simulate peptide solubility using molecular dynamics (GROMACS)?

SCIENCE By mattermodeling.stackexchange.com | 11 hours ago I’m not sure why you would use radius for gyration as a measure of solubility. Radius of gyration roughly measures how “unfolded” (or more accurately, how “stretched out”) a polymer is. Although this may correspond to a higher solvent accessible surface area (which…

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molecular dynamics – How to choose appropriate energy term in GROMACS MD simulation (Lennard-Jones or Coulomb)?

Which is more appropriate for the binding energy? Neither. Obi-Wan voice: “These are not the energies you’re looking for.” If I understand your goal, you’re trying to compare two ligands and determine which is better at binding to a given protein (and, ideally, quantify “how much better” one is compared…

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molecular dynamics – How to manage disk space for Gromacs XTC (trajectory) file output

Is there an option in gmx mdrun to specify where to write the .xtc file? For example I want to specify specific directory path with large disk space. When you use the -deffnm md argument to gmx mdrun, it is assumed that all of the files will have the base…

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[100% Off UDEMY Coupon] – Molecular Dynamic Simulation on Gromacs Software –

Using this 100% off UDEMY Free Coupon Code, you can able to enroll the course: Molecular Dynamic Simulation on Gromacs Software for Free on Udemy.This is a UDEMY Free Promo Code this is totally Free for a Limited Time so enroll soon as possible Molecular Dynamics Simulations ,Gromacs Software ,MD…

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Gromacs: src/gromacs/gmxpreprocess Directory Reference

Directory dependency graph for gmxpreprocess: This browser is not able to show SVG: try Firefox, Chrome, Safari, or Opera instead. Directories directory   tests   Files file   add_par.c   file   add_par.h   file   calch.c   file   calch.h   file   convparm.c   file   convparm.h  …

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Gromacs: gmx::GpuBonded::Impl Class Reference

#include <gromacs/listed-forces/gpubonded-impl.h>   Impl (const gmx_ffparams_t &ffparams, void *streamPtr)   Constructor.     ~Impl ()   Destructor, non-default needed for freeing device-side buffers.   void  updateInteractionListsAndDeviceBuffers (ArrayRef< const int > nbnxnAtomOrder, const t_idef &idef, void *xqDevice, void *forceDevice, void *fshiftDevice)   Update lists of interactions from idef suitable for the…

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Gromacs: gmx::LastStepSignaller Class Reference

#include <gromacs/modularsimulator/signallers.h> Inheritance diagram for gmx::LastStepSignaller: This browser is not able to show SVG: try Firefox, Chrome, Safari, or Opera instead. [legend] Collaboration diagram for gmx::LastStepSignaller: This browser is not able to show SVG: try Firefox, Chrome, Safari, or Opera instead. [legend] Description Element signalling the last step. This element…

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Accepted gromacs 2022~beta2-1 (source) into experimental

—–BEGIN PGP SIGNED MESSAGE—– Hash: SHA256 Format: 1.8 Date: Tue, 07 Dec 2021 19:29:05 -0800 Source: gromacs Architecture: source Version: 2022~beta2-1 Distribution: experimental Urgency: medium Maintainer: Debichem Team <debichem-de…@lists.alioth.debian.org> Changed-By: Nicholas Breen <nbr…@debian.org> Changes: gromacs (2022~beta2-1) experimental; urgency=medium . * New upstream beta release. – gmx_x11.patch: Drop, applied upstream. -…

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Dual AMD EPYC 7773X Flagship Milan-X CPUs Benchmarked, Over 1.5 GB of Total CPU Cache On A Single Server Platform

New benchmarks of AMD’s upcoming Milan-X flagship, the EPYC 7773X CPU, have been submitted to the OpenBenchmarking software suite. AMD EPYC 7773X Milan-X CPUs With Up To 1.6 GB of Total CPU Cache Benchmarked In Dual Socket Server Platform The benchmarks were spotted within the OpenBenchmarking database and consist of…

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Accepted gromacs 2022~beta1-1 (source all amd64) into experimental, experimental

—–BEGIN PGP SIGNED MESSAGE—– Hash: SHA256 Format: 1.8 Date: Fri, 26 Nov 2021 16:24:15 -0800 Source: gromacs Binary: gromacs gromacs-data gromacs-dbgsym libgromacs-dev libgromacs7 libgromacs7-dbgsym libnblib-dev libnblib0 libnblib0-dbgsym Architecture: source all amd64 Version: 2022~beta1-1 Distribution: experimental Urgency: medium Maintainer: Debichem Team <debichem-de…@lists.alioth.debian.org> Changed-By: Nicholas Breen <nbr…@debian.org> Description: gromacs – Molecular dynamics…

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7643-gromacs-tyan-s8252 Benchmarks – OpenBenchmarking.org

2 x AMD EPYC 7643 48-Core testing with a TYAN S8252GM2NE-2T (V2.00.B10 BIOS) and ASPEED 40GB on Ubuntu 20.04 via the Phoronix Test Suite. Compare your own system(s) to this result file with the Phoronix Test Suite by running the command: phoronix-test-suite benchmark 2112014-HOWE-7643GRO17 2 x AMD EPYC 7643 48-Core…

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7713-tyan-b8251-2u4g-gromacs Performance – OpenBenchmarking.org

2 x AMD EPYC 7713 64-Core testing with a TYAN S8251GM2NE-2T (V2.00.B10 BIOS) and ASPEED 40GB on Ubuntu 20.04 via the Phoronix Test Suite. Compare your own system(s) to this result file with the Phoronix Test Suite by running the command: phoronix-test-suite benchmark 2111305-HOWE-7713TYA26 2 x AMD EPYC 7713 64-Core…

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Gromacs: src/gromacs/imd/imdsocket.h File Reference

#include “config.h”#include <netinet/in.h>#include <sys/socket.h> This browser is not able to show SVG: try Firefox, Chrome, Safari, or Opera instead. This browser is not able to show SVG: try Firefox, Chrome, Safari, or Opera instead. Implements the parts of the vmdsock.h interface needed for IMD communication. Author Martin Hoefling, Carsten Kutzner…

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7773X-gromacs Performance – OpenBenchmarking.org

2 x AMD Eng Sample: 100-000000504-04_34/21_N testing with a Supermicro H12DSG-O-CPU (2.1 BIOS) and ASPEED on Ubuntu 20.04 via the Phoronix Test Suite. Compare your own system(s) to this result file with the Phoronix Test Suite by running the command: phoronix-test-suite benchmark 2111268-HOWE-7773XGR31 2 x AMD Eng Sample: 100-000000504-04_34/21_N –…

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7713-gromacs Performance – OpenBenchmarking.org

2 x AMD EPYC 7713 64-Core testing with a Inspur 4.02.06 and ASPEED 40GB on Ubuntu 20.04 via the Phoronix Test Suite. Compare your own system(s) to this result file with the Phoronix Test Suite by running the command: phoronix-test-suite benchmark 2111266-HOWE-7713GRO09 2 x AMD EPYC 7713 64-Core – ASPEED…

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Gromacs-m1pro Benchmarks – OpenBenchmarking.org

Apple M1 Pro testing with a Apple MacBook Pro and Apple M1 Pro on macOS 12.1 via the Phoronix Test Suite. Compare your own system(s) to this result file with the Phoronix Test Suite by running the command: phoronix-test-suite benchmark 2111255-TJ-GROMACSM122 Apple M1 Pro – Apple M1 Pro – Apple…

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Gromacs: src/gromacs/options/optionfiletype.h File Reference

This browser is not able to show SVG: try Firefox, Chrome, Safari, or Opera instead. Defines an enumeration type for specifying file types for options. Author Teemu Murtola teemu.nosp@m..mur.nosp@m.tola@.nosp@m.gmai.nosp@m.l.com enum   gmx::OptionFileType {   eftUnknown, eftTopology, eftTrajectory, eftEnergy,   eftPDB, eftIndex, eftPlot, eftGenericData,   eftOptionFileType_NR }   Purpose of file(s) provided through an…

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HPC-AI Advisory Council Announces the Winners of the 4th APAC HPC-AI Competition

36 Student Teams from Around the Asia Pacific (APAC) Region Participated in the Six-Month Long Competition which included Training and Hands-on Challenges SINGAPORE & SUNNYVALE, Calif., November 18, 2021–(BUSINESS WIRE)–The HPC-AI Advisory Council (HPCAIAC) and National Supercomputing Centre (NSCC) Singapore today announced the university team winners of its annual HPC-AI…

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Gromacs: src/gromacs/mdtypes Directory Reference

Directory dependency graph for mdtypes: This browser is not able to show SVG: try Firefox, Chrome, Safari, or Opera instead. Files file   awh_correlation_history.h   file   awh_history.h   file   awh_params.h   file   commrec.h   file   df_history.cpp   file   df_history.h   file   edsamhistory.h   file…

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Gromacs: src/gromacs/pulling/pull_rotation.h File Reference

#include “gromacs/math/vectypes.h”#include “gromacs/timing/wallcycle.h” This browser is not able to show SVG: try Firefox, Chrome, Safari, or Opera instead. Declares functions to enforce rotational motion upon a group of particles. Author Carsten Kutzner ckutz.nosp@m.ne@g.nosp@m.wdg.d.nosp@m.e void  init_rot (FILE *fplog, t_inputrec *ir, int nfile, const t_filenm fnm[], struct t_commrec *cr, rvec *x, matrix…

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Running 20k simulations in 3 days to accelerate early stage drug discovery

This post contributed by Christian Kniep, Sr. Developer Advocate for HPC and AWS Batch at AWS, Carsten Kutzner, staff scientist at the Max Planck Institute for Biophysical Chemistry, and Vytautas Gapsys, project group leader at the Max Planck Institute for Biophysical Chemistry in Göttingen. Early stage drug discovery helps to identify…

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Gromacs: gmx::LegacyMdrunOptions Class Reference

This class provides the same command-line option functionality to both CLI and API sessions. This class should not exist, but is necessary now to introduce support for the CLI and API without duplicating code. It should be eliminated following the TODOs below. Warning Instances provide lifetime scope for members that…

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Molecular Dynamics Simulation Of Nanocomposites Using Biovia Materials Studio, Lammps And Gromacs

Book Synopsis Molecular Dynamics Simulation of Nanocomposites using BIOVIA Materials Studio, Lammps and Gromacs presents the three major software packages used for the molecular dynamics simulation of nanocomposites. The book explains, in detail, how to use each of these packages, also providing real-world examples that show when each should be…

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Accepted gromacs 2021.4-2 (source) into unstable

—–BEGIN PGP SIGNED MESSAGE—– Hash: SHA256 Format: 1.8 Date: Mon, 08 Nov 2021 18:00:11 -0800 Source: gromacs Architecture: source Version: 2021.4-2 Distribution: unstable Urgency: medium Maintainer: Debichem Team <debichem-de…@lists.alioth.debian.org> Changed-By: Nicholas Breen <nbr…@debian.org> Changes: gromacs (2021.4-2) unstable; urgency=medium . * Cherry-pick upstream merge request 2172, widening tolerance for one build-time…

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Gromacs: gmx::CheckpointHelperBuilder Class Reference

#include <gromacs/modularsimulator/checkpointhelper.h> Description Builder for the checkpoint helper. Public Member Functions   CheckpointHelperBuilder (std::unique_ptr< ReadCheckpointDataHolder > checkpointDataHolder, StartingBehavior startingBehavior, t_commrec *cr)   Constructor.   void  registerClient (ICheckpointHelperClient *client)   Register checkpointing client.   void  setCheckpointHandler (std::unique_ptr< CheckpointHandler > checkpointHandler)   Set CheckpointHandler.   template<typename… Args> std::unique_ptr< CheckpointHelper >  build (Args…

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Accepted gromacs 2021.4-1 (source) into unstable

—–BEGIN PGP SIGNED MESSAGE—– Hash: SHA256 Format: 1.8 Date: Sat, 06 Nov 2021 16:33:33 -0700 Source: gromacs Architecture: source Version: 2021.4-1 Distribution: unstable Urgency: medium Maintainer: Debichem Team <debichem-de…@lists.alioth.debian.org> Changed-By: Nicholas Breen <nbr…@debian.org> Changes: gromacs (2021.4-1) unstable; urgency=medium . * New upstream release. Checksums-Sha1: 0a0b42e03901235bcf31a7739aa57c50c2e18e4a 2985 gromacs_2021.4-1.dsc 56ed2dcec0b62b4749e5ccbf02fabc4c90307477 48541736 gromacs_2021.4.orig-regressiontests.tar.gz…

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gromacs 2021.4 – Download, Browsing & More

gromacs 2021.4 – Download, Browsing & More | Fossies Archive “Fossies” – the Fresh Open Source Software Archive Contents of gromacs-2021.4.tar.gz (5 Nov 09:47, 38023262 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…

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Optimizing price-performance for GROMACS with GPUs

One of the main benefits of AWS is being able to select from over 400+ types of instances for running your high performance computing (HPC) applications. In addition to differences in number of cores, memory, and storage, AWS offers different architectures from Intel, AMD, and our own Arm-based Graviton instances….

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CONVERT PSF to TOP grimaces

namd-l: Re: CONVERT PSF to TOP grimaces I might be a little biased since I wrote TopoGromacs for my own needs, but I think it’s a fine way to generate the .top file GROMACS expects. This defines the system topology and parameters, which are combined with a .mdp file into…

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Virtual Double-System Single-Box for Absolute Dissociation Free Energy Calculations in GROMACS

We describe a step-by-step protocol for the computation of absolute dissociation free energy with GROMACS code and PLUMED library, which exploits a combination of advanced sampling techniques and nonequilibrium alchemical methodologies. The computational protocol has been automated through an open source Python middleware (HPC_Drug) which allows one to set up…

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Gromacs: gmx::StandardInputStream Class Reference

#include <gromacs/utility/filestream.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] Text input stream implementation for reading from stdin. Implementations for the TextInputStream methods throw FileIOError on…

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Debian — Details of package libgromacs-dev in bullseye

GROMACS molecular dynamics sim, development kit 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 ERROR

GROMACS ERROR 0 I was running the GROMACS command (gmx grompp -f nvt.mdp -c proteinem.gro -r proteinem.gro -p protein.top -n index.ndx -o nvt.tpr -maxwarn 1) along with change in temperature in mdp files and got the error (Fatal error: An input file contains a line longer than 4095 characters, while…

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Gromacs: gmx::test::ModuleSelection Class Reference

#include <gromacs/coordinateio/tests/coordinate_test.h> Inheritance diagram for gmx::test::ModuleSelection: This browser is not able to show SVG: try Firefox, Chrome, Safari, or Opera instead. [legend] Description Helper class for tests that need an initialized selection. Member Function Documentation void gmx::test::ModuleSelection::addOptionForSelection ( Selection *  sel, bool  useValid  ) inline Method to add a valid…

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NVIDIA-SMI has failed because it couldn’t communicate with the NVIDIA driver. Centos 7 – CUDA Setup and Installation

HiFor installation of gromacs in Tesla C2050 workstation, with recommendation of CUDA 8.0 [Which recent cuda + gromacs versions combo suitable for Tesla C2050 workstation – User discussions – GROMACS forums] (Which recent cuda + gromacs versions combo suitable for Tesla C2050 workstation – User discussions – GROMACS forums) ….

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GROMACS Deployment through Resource Manager workshop

About This Workshop GROMACS is a versatile software package to perform molecular dynamics, and is used to simulate different equations with hundreds to millions of particles.This Runbook will take you through the process of deploying GROMACS Software on Oracle Cloud. In this particular demo, we are going to achieve this…

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Gromacs: gmx::SimulationSignal Class Reference

POD-style object used by mdrun ranks to set and receive signals within and between simulations. Keep in mind that the values of signals are transmitted to other ranks through an MPI_Reduce after casting them to a real (so the signals can be sent together with other data). This means that…

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Gromacs: gmx::CommandLineCommonOptionsHolder Class Reference

Public Member Functions void  initOptions ()   Initializes the common options.   bool  finishOptions ()   Finishes option parsing. More…   void  adjustFromSettings (const CommandLineModuleSettings &settings)   Adjust defaults based on module settings.   Options *  options ()   Returns the internal Options object.   const BinaryInformationSettings &  binaryInfoSettings ()…

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Accepted gromacs 2021.3-4 (source) into unstable

—–BEGIN PGP SIGNED MESSAGE—– Hash: SHA256 Format: 1.8 Date: Sat, 23 Oct 2021 11:18:36 -0700 Source: gromacs Architecture: source Version: 2021.3-4 Distribution: unstable Urgency: medium Maintainer: Debichem Team <debichem-de…@lists.alioth.debian.org> Changed-By: Nicholas Breen <nbr…@debian.org> Closes: 997067 Changes: gromacs (2021.3-4) unstable; urgency=medium . * Add Build-Depends-Indep: tex-gyre. (Closes: #997067) Checksums-Sha1: f5daaf2a26ab58cf451162d56faf6db17c9af590 2985…

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Gromacs: Class Members

Here is a list of all documented class members with links to the class documentation for each member: – m – m : gmx_ana_pos_t m_elements : gmx::EnumerationArray< EnumType, DataType, ArraySize > machine() : gmx::HardwareTopology makeCumulative() : gmx::AbstractAverageHistogram makeMDAtoms : gmx::MDAtoms makeTable() : gmx::TabulatedNormalDistribution< RealType, tableBits > malloc() : gmx::AlignedAllocationPolicy ,…

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Running GROMACS on GPU instances

Comparing the performance of real applications across different Amazon Elastic Compute Cloud (Amazon EC2) instance types is the best way we’ve found for finding optimal configurations for HPC applications here at AWS. Previously, we wrote about price-performance optimizations for GROMACS that showed how the GROMACS molecular dynamics simulation runs on single instances,…

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Hands-on Molecular Dynamics Simulations Workshop with research computing set for Friday | E-News

Join the Research Computing Team on Zoom for a two-hour long workshop on molecular dynamics simulations Friday (Oct. 22) at 1 p.m. This workshop will cover the three MD engines currently available on WVU HPC resources: NAMD, AMBER and GROMACS.  This workshop is meant for beginners and intermediate users of…

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Not being able to run Gromacs simulations or higher nodes

I am running Gromacs software on Devcloud JupyterLab environment. Devclouud is restricting to use no of nodes >2. Whenever I am trying to run with nodes=3:ppn=2 in qsub command it returns an error like “qsub: submit error (Job exceeds queue resource limits MSG=job violates queue/server max resource limits)” . How to solve this…

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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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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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