Tag: GROMACS

Error when adding new residue to hdb (CHARMM36) – User discussions

dom June 26, 2022, 2:05am #1 GROMACS version:2022.2GROMACS modification: No I am adding a new protein residue to the CHARMM36 forcefield (July 2021). As per the instructions in the GROMACS manual (“Adding a Residue to a Force Field”), I modified residuetypes.dat, aminoacids.rtp, and aminoacids.hdb with the new residue entry. It…

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ERROR No such moleculetype NA – User discussions

GROMACS version:GROMACS modification: Yes/No I got this errorwhen I run the line: gmx grompp -f em.mdp -c solv_ions.gro -p topol.top -o em.tpr -maxwarn 10in the topol.top there is 3 NA atoms 🙂 GROMACS – gmx grompp, 2020.1-Ubuntu-2020.1-1 (-: GROMACS is written by: Emile Apol Rossen Apostolov Paul Bauer Herman J.C….

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Molecular Dynamics Simulation Software Market by 2029

New Jersey (United States) – A2Z Market Research published new research on Global Molecular Dynamics Simulation Software covering the micro-level of analysis by competitors and key business segments (2022-2029). The Global Molecular Dynamics Simulation Software explores a comprehensive study on various segments like opportunities, size, development, innovation, sales, and overall…

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Creating nacl in water system – User discussions

GROMACS version: 2018.6GROMACS modification: No I am very new to using gromacs, so I would appreciate any input.I am trying to set up a system of NaCl (JC) in water(spce) . I was able to run the tutorial simulation of lysozome in water. But in this the topology file was…

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Porting GROMACS Across Heterogeneous Architectures

Porting GROMACS Across Heterogeneous Architectures In this second episode about GROMACS, one of the world’s most widely used open source molecular dynamics (MD) applications, we explore the quest to simplify portable, performant programming with Erik Lindahl, Biophysics Professor at Stockholm University & KTH Royal Institute of Technology, and Roland Schulz,…

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Regarding the use of -table and -tablep – User discussions

GROMACS version: 2018.3GROMACS modification: No Hi, I am trying to simulate a polymer-water system where the polymer beads interact by Weeks-Chandler-Andersen potential and all the other non-bonded interactions are LJ type. I have two tabulated potential files: (i) table.xvg (for LJ) and (ii) table_P_P.xvg (for WCA). In the .mdp file…

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How to calculate total interaction energy between protein and polyethylene surface – User discussions

Teabo May 9, 2022, 4:03am #1 GROMACS version: Gromacs 2018GROMACS modification: NoHere post your questionDear all,I have a system including one protein and one polyethylene layer. I wonder how to calculate the interaction energy between the protein and the polyethylene layer, should I use gmx enemat? Or could anyone suggest…

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[gmx-users] Gromacs 5.1 – trouble with insert-molecules

I think I answered this a week ago. Post by Dan GilHi,I am upgrading from gromacs 4.6 to gromacs 5.1. Gromacs 4.6 had “genbox,”which I was able to use without a problem.With gromacs 5.1, I am using insert-molecules to generate my initialconfiguration containing water, ethanol, and a lennard-jones particle whichI…

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Accepted gromacs 2022.1-1 (source) into experimental

—–BEGIN PGP SIGNED MESSAGE—– Hash: SHA256 Format: 1.8 Date: Fri, 22 Apr 2022 18:22:17 -0700 Source: gromacs Architecture: source Version: 2022.1-1 Distribution: experimental Urgency: medium Maintainer: Debichem Team <debichem-de…@lists.alioth.debian.org> Changed-By: Nicholas Breen <nbr…@debian.org> Closes: 1009383 Changes: gromacs (2022.1-1) experimental; urgency=medium . * New upstream release. * Restore mdrun-test-timeout.patch, to handle…

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SwissDock and Autodock Vina results comparison : comp_chem

Hi! I’m a chemistry undergrad. For my research, I performed docking using Autodock Vina. For further validation, I tried docking using SwissDock too. But now, the two programs give different results. They predict different ligands to give the most favorable binding. I read that Autodock is more reliable. So, should…

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Molecular Dynamics Software Market Growing Popularity & Emerging Trends

The latest independent research document on Molecular Dynamics Software examine investment in Market. It describes how companies deploying these technologies across various industry verticals aim to explore its potential to become a major business disrupter. The Molecular Dynamics Software study eludes very useful reviews & strategic assessment including the generic market…

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Density profile along the interface normal – User discussions

Dear all,I’d like to observe how density varies within the box, therefore could someone please explain how to find density within each of the slices of a simulation box formed by slicing the simulation cell into 1 angstrom-partitions along the z axis? Sasha April 15, 2022, 9:48am #2 gmx density:…

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Bioinformatics Software Market Outlook: Post Covid-19 Scenario by 2029

California (United States) – The Bioinformatics Software Market Research Report is a professional asset that provides dynamic and statistical insights into regional and global markets. It includes a comprehensive study of the current scenario to safeguard the trends and prospects of the market. Bioinformatics Software Research reports also track future…

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How to combine OPLS-AA with Berger lipids? Links in tutorial dead – User discussions

Isolde April 13, 2022, 2:15am #1 GROMACS version: 2022GROMACS modification: No Greetings! I would like to simulate a small molecule (described by OPLS-AA) interacting with a POPC bilayer (Berger lipids). However, the links in the GROMACS membrane tutorial (see below) that should lead to instructions on how exactly to combine…

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No default type errors -NH2 and COO- amino acid termini patches for pH 10 simulations – User discussions

GROMACS version:2022GROMACS modification: NoMuch thanks for any help and guidance on these errors – I am studying mixtures of amino acids at pH 10; at this pH the N-term is neutral NH2 and the C-term is negative COO-. I am using the charmm27 force field to parametrize and patch each…

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GROMACS+CP2K Single vs Double Precision – User discussions

cbl123 April 4, 2022, 8:38pm #1 GROMACS version: 2022GROMACS modification: Yes/No (CP2K) Hello dear users and devs, I would like to know if there’s major implications in the accuracy of my calculations if I use single precision instead of the recommended double precision for QM/MM calculations with Gromacs 2022+CP2K. Thanks…

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Loading environment modules on a cluster from my python script

I recently ran into this. A simple way around this would be to include the dependencies before the command you want, and separate them with a semi-colon cmd = ‘module load intel/2016.4; “gromacs command”‘ p = sub.Popen(cmd, shell=True, stderr = sub.STDOUT, stdout = sub.PIPE).communicate()[0] where “gromacs command” represents however you…

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Double precision on gro file using editconf – User discussions

GROMACS version:2022.1GROMACS modification: NoIs there a way to keep the position coordinate in DP? The gro file seems to revert back to SP when it get converted from pdb to gro by editconf. I can rewrite them into DP but I do not know how to keep DP when the…

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[gmx-users] template.c is needed for Gromacs 5.0

Hi, Unfortunately, no. The whole project has been moving to C++ for some years.Writing the template in object-oriented C would look (and work) even worse😉 If you’ve got some specific feedback about what’s hard to understand,we’re happy to consider improvements! 🙂 Mark Post by BertHi all,I used to write my…

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Understanding the implementation of the virtual sites in gromacs – User discussions

GROMACS version: 2020.5GROMACS modification: NoI am building a CG model using virtual particles. I defined the virtual particle on the basis of the position of the neighboring particles and distributed the mass of that particular particle which I want to make virtual to the corresponding neighboring particles. My understanding is…

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Sign Up Log In Log In Popular “make check” Test 1 fails for Gromacs 2022User discussions DNA ending effectUser discussions GROMACS 2022 official releaseAnnouncements Basic questions about constant pH simulationUser discussions File input/output error: tprout.tprUser discussions 2022 Regression Test TimeoutsUser discussions Why is mpi thinking gromacs args are for mpi?User…

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Gromacs performance on GPU – User discussions

GROMACS version: 2022GROMACS modification: Yes/No Hi! I am checking the performance of my fresh Gromacs installation on a new PC. I have the newest Gromcas compiled (Linux Mint) using the basic scheme from the manual with added support for Nvidia GPU (CUDA, 11.60). CPU is AMD Ryzen 9 5950X (16…

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Nvt.mdp killed in 7 min – User discussions

GROMACS version:2022+cp2k interface basically, my system is small but I couldn’t start nvt job. Can you I help me, what I am doing wrong?Thank you in advance I am taking that error : Command line:gmx_cp2k mdrun -s nvt.tpr -v -deffnm nvt Compiled SIMD: AVX_256, but for this host/run AVX2_256 might…

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Gromacs: src/gromacs/selection/selmethod.cpp File Reference

#include “gmxpre.h” #include “selmethod.h” #include <cctype> #include <cstdarg> #include “gromacs/utility/arraysize.h” #include “gromacs/utility/cstringutil.h” #include “gromacs/utility/exceptions.h” #include “gromacs/utility/stringutil.h” #include “selmethod-impl.h” #include “symrec.h” This browser is not able to show SVG: try Firefox, Chrome, Safari, or Opera instead. Implements functions in selmethod.h. Author Teemu Murtola teemu.nosp@m..mur.nosp@m.tola@.nosp@m.gmai.nosp@m.l.com static void  report_error (FILE *fp, const char…

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Fatal error: Invalid line in complex.gro for atom 5185: 9.36900 9.36900 16.01200 – User discussions

GROMACS version: 2020.1GROMACS modification: NoHello everyone, i get error message like this when define unit cell gmx editconf -f complex.gro -o newbox.gro -bt cubic -d 1.5 Fatal error:Invalid line in complex.gro for atom 5185: 9.36900 9.36900 16.01200Previously I have also done simulations with other ligands and it worked. anyone can…

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Nvt.tpr -I couldn’t manage my nvt.tpr – User discussions

GROMACS version:2022-cp2k interface I couldn’t manage my nvt.tpr I tried to fix problem but I couldn’t. gmx_cp2k grompp -f nvt.mdp -c confout.gro -r confout.gro -p topol.top -n index.ndx -o nvt.tpr nvt.mdb file :; md-nvt.mdp – used as input into grompp to generate nma-nvt.tprintegrator = md ; MD using leap-frog integratordt…

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Gmxapi gromacs 2022 error – User discussions

. /path/to/gromacs/bin/GMXRC You used the actual installation path here, right? ╰─> [124 lines of output] We can’t help without the full output. Please copy the raw text from the terminal window. Note that you can format the terminal output in the forum post either by using the </> button or…

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Issue with gmx extract-cluster – User discussions

GROMACS version: 2020.1GROMACS modification: No Hello Gromacs users, I need to extract a set of frames from my trajectory and I have the index of these frames (the frame number, not time). With gromacs version before 2020, I used to create an index file and then extract the conformations with…

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Gromacs: gmx::DomDecHelper Class Reference

Infrastructure element responsible for domain decomposition. This encapsulates the function call to domain decomposition, which is important for performance but outside of the current scope of the modular simulator project. This relies on legacy data structures for the state and the topology. This element does not implement the ISimulatorElement interface,…

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Change of protein-protein-interaction free energy upon ligand binding (procedure and controls) – User discussions

GROMACS version: 2021.1GROMACS modification: No Dear Gromacs and simulation community, in the course of my master’s thesis, I want to determine the protein-protein-binding free energy between two GTPases using PMF calculations via umbrella sampling. Especially I am interested in the contribution of the bound nucleotides (one per protein) which are…

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trollchu | coder – Coder Social

Qingzhao’s Projects AI-learns-to-play-the-dino-game AsFem A Simple Finite Element Method program (AsFem) aten Molecular / atomic coordinate editor atomman Atomistic Manipulation Toolkit awesome-python-chemistry A curated list of Python packages related to chemistry awesome-python-MD cantera Chemical kinetics, thermodynamics, and transport tool suite CFDPython A sequence of Jupyter notebooks featuring the “12 Steps…

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GROMACS – SBGrid Consortium – Supported Software

Usage Notes SBGrid Usage Info GROMACS is GPU-accelerated using Nvidia CUDA on Linux. For general information on running GPU accelerated applications from SBGrid, please see here : sbgrid.org/wiki/gpu CUDA builds of GROMACS are designated by a ‘_cu’ suffix in the version of the application. For example, 2020.2_cu9.2.88 is linked against…

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Regarding the use of WCA and Attractive inteactions simultaneously – User discussions

GROMACS version: 2018.3GROMACS modification: No Hello Gromacs users, I am trying to simulate a system where some of the particles (type-A) obey WCA potential and some (type-B) obey an attractive potential (user defined). And there A-B interaction follows another (user defined) poential form. I have used tabulated potentials but not…

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LJ parameters – User discussions

GROMACS version: 2021.3GROMACS modification: NoHere post your question I have a very basic question on parameterization of non-bonded parameters (LJ) of atoms. The target system is a cluster/aggregate of metal atoms. From experimental data, I can get the atomic radius and vdw radius of the atoms. However, looking at the…

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Issue with segmentation fault – User discussions

GROMACS version: 2021.2, 2019.6GROMACS modification: YesHere post your question I am facing a segmentation fault issue with GROMACS patched with plumed and I was wondering if you could help me. I am trying to run a replica averaged MD simulation by calculating the backbone chemical shifts for a protein (using…

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molecular dynamics – How to generate a .tpr file from a .pdb or .xyz file in gromacs

For generating a tpr file, you need a topology file (.top), a coordinate file (.gro/.pdb) and a input parameter file (.mdp). Assuming, you are working with amber forcefield (a99ffSBdisp), Here’s how I do it. gmx pdb2gmx -ff a99SBdisp -f yourpdbfile.pdb -o water_1.gro -ignh -p topol.top gmx grompp -f water.mdp -c…

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How to generate a free energy Ramachandran plot from a GROMACS MD trajectory if protein has more than 2 residues? : comp_chem

I ran some REMD calculations with GROMACS and wish to create a plot which depicts the free energies of the different regions on the Ramachandran plot of my protein at a specific temperature, similar to figure 2 in the following paper below. Article Antifreeze Glycoproteins Bind Reversibly to Ice via…

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Gromacs: gmx::analysismodules::anonymous_namespace{rdf.cpp}::Rdf Class Reference

Public Member Functions virtual void  initOptions (IOptionsContainer *options, TrajectoryAnalysisSettings *settings)   Initializes options understood by the module. More…   virtual void  optionsFinished (TrajectoryAnalysisSettings *settings)   Called after all option values have been set. More…   virtual void  initAnalysis (const TrajectoryAnalysisSettings &settings, const TopologyInformation &top)   Initializes the analysis. More…  …

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[gmx-users] why not coordinates from cpt file

Post by gromacs queryHi allI have very simple query. While continuing simulations why we need to use*.gro (-c) with grompp as *.cpt (-t) has all the information (as checkedwith gmxcheck)?cpt file should suffice all the purposes. I tried using grompp providing -t*.cpt file but without -c *.gro file, it does…

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[gmx-users] Adaptive Biasing Force method

Post by k***@mech.sharif.irDear GROMACS usersIs there any way� to employ the adaptive biasing force (ABF) methodwith GROMACS ?! If so,� could you please introduce me a tutorial orarticle about it ? I really appreciate it. Available features are described in the manual. Tutorials are found via Google. -Justin—================================================== Justin A….

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[gmx-users] sudden jumps in RMSD etc.

Hi all, I am doing duplicate MD simulations with a protein-ligand system. After processing one trajectory by trjconv with the optioin -pbc nojump, Istill find abrupt jumps (on the scale of nm) in RMSDs and COM distances. Then I tried -pbc mol -ur compact, which did not work. And then…

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Gromacs: src/gromacs/nbnxm/kernels_reference Directory Reference

Directory dependency graph for kernels_reference: This browser is not able to show SVG: try Firefox, Chrome, Safari, or Opera instead. Files file   kernel_gpu_ref.cpp   file   kernel_gpu_ref.h   Declares GPU reference kernel.   file   kernel_ref.cpp   file   kernel_ref.h   Declares CPU reference kernels.   file   kernel_ref_includes.h…

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Accepted gromacs 2022~rc1-1 (source) into experimental

—–BEGIN PGP SIGNED MESSAGE—– Hash: SHA256 Format: 1.8 Date: Sat, 29 Jan 2022 10:08:31 -0800 Source: gromacs Architecture: source Version: 2022~rc1-1 Distribution: experimental Urgency: medium Maintainer: Debichem Team <debichem-de…@lists.alioth.debian.org> Changed-By: Nicholas Breen <nbr…@debian.org> Changes: gromacs (2022~rc1-1) experimental; urgency=medium . * New upstream release candidate. * Drop hppa-disable-ewaldunittest.patch. * Set build…

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[gmx-users] Regarding combination rules in gromos53a6 ff

Dear GROMACS users,I want to use the geometric mean of both sigma (sigma i sigmaj)andepsilon(epsilon i epsilon j) as a combination rule in my simulation.According to the combination rules in the manual, the combination 3incorporates Vii=sigma and Wii= epsilon along with geometric mean of Ci(6)Cj(6) and Ci(12)Cj(12) terms.So can I…

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[gmx-users] Is such hardware suitable for gromacs

Your mail looks like spam at first glance. Surely. They can be used to run Gromacs. In fact, Gromacs welcomes bothIntel and AMD’ modern CPU with SIMD capability. To build a small cluster, you also need some networking devices: a GBether switch and some good cables. Rest is software installation…

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[gmx-users] Why gyration radius keep dropping?

Post by ZHANG ChengDear Gromacs,I am running MD at 500 K for my protein.I used this to analyse the gyration radiusecho 1 | gmx gyrate -s md_0_1.tpr -f md_0_1_noPBC.xtc -o gyrate.xvgI thought the radius should keep increase, as the protein unfolds at high temperature. However, all my repeats showed a…

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Adding ions ‘gmx grompp’ creates error “Atomtype ca not found” for ligand generated with GAFF – User discussions

GROMACS version: 2018GROMACS modification: No Hello, I am trying to run 200ns on protein-ligand complex and then calculate MMPBSA for the last 100 ns generated frames. I had some problems with ligand parameterization with cgenff, hence I used gaff…I have: GAFF to generate parameters for the ligand acpype to convert…

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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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