Categories
Tag: GROMACS
Scaling of MD with domain decomposition on JUWELS Cluster – Developers discussions
GROMACS version: 2024-dev-20240201-787d96c7a9-unknownGROMACS modification: YesI’m conducting some performance tests on the JUWELS Cluster, trying to see the improvement in performance that DD can bring within a single node. GROMACS build infoHere, GROMACS was built using GCC v11.4.0, uses OpenMP and OpenMPI v4.1.5, and builds its own FFTW v3.3.8. JUWELS Cluster…
A Simple Overview for Proteins Molecular Dynamics Simulations Using GROMACS
About Gromacs – Gromacs. s.d. Consulté le 5 mai 2023. www.gromacs.org/About_Gromacs Baker, D., Sali, A.: Protein structure prediction and structural genomics. Science 294(5540), 93–96 (2001). doi.org/10.1126/science.1065659 Beckstein, O., et al.: Ion channel gating: insights via molecular simulations. FEBS Lett. 555(1), 85–90 (2003). doi.org/10.1016/s0014-5793(03)01151-7 CrossRef Google Scholar Bowman, A.L., Ridder, L.,…
Gromacs: gmx::BerendsenTemperatureCoupling Class Reference
Public Member Functions real apply (Step step, int temperatureGroup, real currentKineticEnergy, real currentTemperature, const TemperatureCouplingData &temperatureCouplingData) override Apply the v-rescale temperature control. void connectWithPropagator (const PropagatorThermostatConnection &connectionData, int numTemperatureGroups) override Connect with propagator – Berendsen only scales start step velocities. void writeCheckpoint (std::optional< WriteCheckpointData > checkpointData,…
gmx rotacf – GROMACS 2024 documentation
Description# gmx rotacf calculates the rotational correlation function for molecules. Atom triplets (i,j,k) must be given in the index file, defining two vectors ij and jk. The rotational ACF is calculated as the autocorrelation function of the vector n = ij x jk, i.e. the cross product of the two…
gmx solvate – GROMACS 2023.4 documentation
Description gmx solvate can do one of 2 things: 1) Generate a box of solvent. Specify -cs and -box. Or specify -cs and -cp with a structure file with a box, but without atoms. 2) Solvate a solute configuration, e.g. a protein, in a bath of solvent molecules. Specify -cp…
Molecular Dynamics Software Market to Witness Revolutionary
Molecular Dynamics Software Market Global “Molecular Dynamics Software Market” Research report is an in-depth study of the market Analysis. Along with the most recent patterns and figures that uncovers a wide examination of the market offer. This report provides exhaustive coverage on geographical segmentation, latest demand scope, growth rate analysis…
Breaking a ligand with umbrella sampling – User discussions
ryanm January 19, 2024, 6:40pm 1 GROMACS version: 2022GROMACS modification: YesHere post your questionCan GROMACS umbrella sampling break two bonded atoms in a ligand? Example: using umbrella sampling to show the maximum force to break the carbon and oxygen bond in carbon dioxide molecule. Bonds cannot break or form in…
GPU support and installation – User discussions
tebg January 19, 2024, 8:51am 1 GROMACS version: 2023.3GROMACS modification: Yes (I think??) I’ve just started setting up a new PC with the main goal of running MD simulations, and I’m trying to test out a simple membrane simulation generated by CHARMM-GUI. I installed GROMACS with GPU support, but I…
Gromacs: gmx::test::anonymous_namespace{observablesreducer.cpp}::Subscriber Class Reference
This browser is not able to show SVG: try Firefox, Chrome, Safari, or Opera instead. [legend] Helper class that models an MD module that needs to make a subscription to ObservablesReducer. static constexpr int s_subscriberBufferMinimumSize = 3 Ensure that each subscriber sends an interesting amount of data. static…
Gmxmmpbsa energy part – User discussions
GROMACS version:2022.3GROMACS modification: Yes/NoHere post your questionPreProcessorError: Could not find gromos54a7_atb.ff/forcefield.itpI have runned my md and obtained all the files now on dealing with the binding energy part using gmxmmpbsa I am experiencing error such that gromos54a7_atb.ff/forcefield.itp could not find. I have included this in the topol file and my…
molecular dynamics – Is water penetration and fatty acid dissolution reasonable when Gromacs modelling of an aqueous lipid bilayer?
as mentioned, I’m building a molecular dynamics simulation of decanoic acid and decanoate (with neutralising sodium cations) in water. I’ve minimized and equilibrated the simulation up to 295 K and I’ve generated a little movie of the run (0.002 ns steps for about 1 ms). I have noticed a couple…
Error during production MDrun – User discussions
SP06 January 1, 2024, 6:11am 1 GROMACS version:2021.4GROMACS modification: Yes/NoHere post your question I am simulating my protein in cyclohexane solvent. On the final production MD run, i got the following error-Fatal error:The X-size of the box (5.875432) times the triclinic skew factor (1.000000) issmaller than the number of DD…
Protein at biphase interface – User discussions
SP06 January 1, 2024, 4:36am 1 GROMACS version:2021.4GROMACS modification: Yes/NoHere post your question : I want to simulate my protein at water-cyclohexane interface. Can I use gmx insert-molecules to insert cyclohexane molecules in a box with protein centered in it, and then add water, instead of adding a pre-equilibrated box…
Gromacs: gmx::IntegerOptionStorage Class Reference
Converts, validates, and stores integer values. IntegerOptionStorage (const IntegerOption &settings) Initializes the storage from option settings. More… virtual OptionInfo & optionInfo () Returns an option info object corresponding to this option. virtual std::string typeString () const Returns a short string describing the type of…
Gromacs: gmx::IFileInputRedirector Class Reference
Allows overriding file existence checks from code that supports it. The calling code should take in this interface and use the methods in it all file system operations that need to support this redirection. This allows tests to override the file existence checks without actually using the file system. See…
Generate topology file for glucose – User discussions
horlust December 29, 2023, 10:15am 1 GROMACS version: 2021.4-2GROMACS modification: No Hello everyone! I am fairly new to GROMACS. I’ve been able to successfully run simulations for some small molecules with the OPLS-AA force field. My problem has always been the generation of the topology files. Using pdb2gmx seems impossible…
Installation with GPU – User discussions
GROMACS version: 2023.3GROMACS modification: Yes/NoHere post your question Im trying to install gromacs with SYCL GPU suport using $ cmake … -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=SYCL -DGMX_SYCL_HIPSYCL=on but I got the error CMake Error at cmake/gmxManageSYCL.cmake:77 (message):HipSYCL build requires Clang compiler, but GNU is usedCall Stack (most recent call first):CMakeLists.txt:667 (include) and…
Running GROMACS with OpenCL on accelerator – User discussions
Aastha December 19, 2023, 11:23am 1 GROMACS version:2023.3GROMACS modification: YesHere post your questionI am trying to run GROMACS on an accelerator connected to PCI bus.I made the following modifications to the code: changed CL_DEVICE_TYPE_GPU to CL_DEVICE_TYPE_ALL Added my accelerator vendorcheckGpu returns value TRUE, so the dummy kernel is able to…
molecular dynamics – How do we calculate diffusion coefficient when GROMACS MSD graph with two slopes?
I calculated the MSD using the gmx msd -f run05.part0005.xtc -s run05.tpr -o msd_200-250ns.xvg. As a result, I got a graph with 2 slopes as attached. In the MD simulation, I followed a simulated annealing schedule for every 25 ns. Since I get the kink at 25 ns, I believe…
Lipid vesicle(CHARMM Gui files) simulation in GROMACS – User discussions
GROMACS version: 2022.1 and 2020GROMACS modification: Yes/NoHere post your questionHello, I am trying to simulate Lipid based vesicle in GROMACS on Frontera super-computer. The following command I am using to run the simulation. But I am getting error messages. Since I am new I don’t understand the error message perfectly….
How to generate topology for Graphene molecule from .gro file using GROMACS program? – User discussions
vikas28 December 18, 2023, 11:31am 1 GROMACS version: GROMACS/2022.4-fosscuda-2020bGROMACS modification: Yes/NoHere post your questionGreetings, everybody. I have generated a graphene sheet using the VMD program and saved the resulting file in the .gro format. Now I would like to use the GROMACS program to model the interaction between graphene and…
Roto-translational constraints in GROMACS – User discussions
rcrha December 15, 2023, 8:39pm 1 GROMACS version: 2020GROMACS modification: No Dear all, is it possible to use the roto-translational constraints of the solute in GROMACS? I expect that it should be because the original algorithm was published by GROMACS developers. I need to simulate a big non-spherical protein in…
Simulating Histidine Protonation in GROMACS – Beginner Seeking Guidance – User discussions
Hello GROMACS community, I am a total beginner in using GROMACS, and I’m currently working on a project where I need to simulate the protonation state change of histidine residues in a protein, specifically to simulate an acidic environment where histidines gain a proton (NH3+). I have downloaded a protein…
The initial estimative of -nt parameter – User discussions
GROMACS version: 2022.6GROMACS modification: NoHi, community.I would like to know, how gromacs calculate an initial estimate for number of threads used on mdrun? For example, when run this command “gmx mdrun -deffnm md_0_1 -nb gpu” , for system 1, i can see all my 24 threads been using. Nonetheless, when…
Computational Electrophysiology index error – User discussions
btam125 December 15, 2023, 6:19am 1 GROMACS version: 2021GROMACS modification: NoHere post your question Dear all, I am performing a Computational Electrophsiology simulation between 2 membrane. I want to see how the potassium ion crossing the channel and using the swapping to ensure A side has more K ion than…
Gmx mdrun -deffnm NVT – User discussions
GROMACS version:2018.1GROMACS modification: NoI am getting the below error when I giving the command “gmx mdrun -deffnm NVT” Too many LINCS warnings (1000)If you know what you are doing you can adjust the lincs warning threshold inyour mdp fileor set the environment variable GMX_MAXCONSTRWARN to -1,but normally it is better…
Globus and GROMACS changes | PSC
Following this week’s maintenance period on Bridges-2, the following changes have been made. Globus For Globus/GridFTP transfers to/from Bridges-2, please use the new endpoint labelled “PSC Bridges-2 Globus Connect Server 5 Endpoint”. The new Globus CLI endpoint’s UUID is ca35a4c4-6e61-4aaa-8bc1-67b812c1f337. GROMACS If you are a user of Gromacs, you…
Error in MD simulation – User discussions
GROMACS version:2021.7GROMACS modification: NoHere post your questionHello everyone,I’m trying to perform a MD simulation on a protein-ligand complex in acetonitrile as solvent at 45C but it seems there is something wrong with my system since this error pops up.Can anyone please help?**” WARNING: Listed nonbonded interaction between particles 887 and…
Unable to execute the solvate command – User discussions
b220009 December 14, 2023, 12:21am 1 I am doing the part 1:lysosome in water of the tutoriol from the official website Lysozyme in Water, and there is part in solvation where it requires to use the solvate command. However, my GROMACS software is unable to execute it. What are the…
LP pseudo-atom is not supported
Hi, I want to perform MMPBSA for complex file Command: gmx_MMPBSA -O -i mmpbsa.in -cs md_100.tpr -ct md_center.xtc -ci index.ndx -cg 1 13 -cp topol.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv Error: [INFO ] Starting gmx_MMPBSA v1.6.2 [INFO ] Command-line gmx_MMPBSA -O -i mmpbsa.in -cs md_100.tpr -ct md_center.xtc -ci index.ndx -cg 1…
Specifying time length of protein simulation – User discussions
cjbraz December 13, 2023, 7:56pm 1 GROMACS version: 2023.2GROMACS modification: Yes (GMX_OPENMP_MAX_THREADS = 128)Here post your question Hello, the below linked post is a little older version than my version of GROMACS but I would like to get an answer to this post’s question. Running the linked production script only…
Wall simulations with GPU – User discussions
stephan December 13, 2023, 4:46am 1 GROMACS version: 2022.3GROMACS modification: No Dear all, I want to run a simulation with two repulsive walls to keep the system finite in z while having non-periodic boundary conditions in that dimension.Everything works fine except when offloading bonding interactions to the GPU. I think…
Query about Atom Index Ordering in GROMACS 2021.0 and 2023.3 – Developers discussions
Lorien December 12, 2023, 10:55am 1 Hello. I am developing a constraint algorithm and primarily working with GROMACS 2021.0. In executions without domain decomposition and with constraints set to all-bonds, the atom indices appear to follow an order similar to that in the PDB file. For instance, in simulations involving…
Command to run gromacs in parallel – User discussions
cjbraz December 11, 2023, 5:06pm 1 GROMACS version: 2023.2GROMACS modification: Yes/NoHere post your question Hello all. I have used CHARMM-GUI solvent builder to print out a script I can use in a protein simulation. I am able to run the script successfully, but would like to run the full script…
Faster simulation – User discussions
SP06 December 12, 2023, 9:19am 1 GROMACS version: 2021.4GROMACS modification: Yes/NoHere post your question : I want to run a simulation for 100 ns and more. But it’s taking too much time on my PC/laptop. Is there any way to run the simulation faster on my desktop/latop instead of supercomputer?…
A Comprehensive Overview for the 2024-2031 Period| With 117 Pages
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How to restrain to some specified waters for OPC model – User discussions
Shin December 11, 2023, 1:24am 1 GROMACS version:2021.6GROMACS modification: NoHere post your questionDear Gromacs usersI have the same problem as inHow to treat specific water molecules as ligand?. I’m setting .top file for MD simulation with OPC model for water.I want to use positional constraints on the three waters(name: FIX)…
Running GROMACS efficiently on LUMI
BioExcel CoE, in collaboration with CSC – IT Center for Science and PDC Center for High-Performance Computing, will host a two-day online workshop on efficiently running GROMACS on LUMI on 24-25 January 2024. This course is designed to provide practical tips on how to run GROMACS simulations efficiently on LUMI-G…
Comparison between two MD – User discussions
lilian December 10, 2023, 6:27am 1 GROMACS version: 2020GROMACS modification: No Hi gmx users,I did two simulations. 1) polymer(x)-drug and 2) polymer(y)-drug. In these two simulations, the polymers are different but the drugs are the same.According to the structure and shape of the polymers, the size of the box is…
AWH very large free energy barriers – User discussions
Noob December 10, 2023, 12:43am 1 GROMACS version: 2023.3GROMACS modification: NoI have been trying to run a Free energy simulation using AWH and no matter what I set some of the values too I keep getting the same error: ——————————————————- Program: gmx mdrun, version 2023.3 Source file: src/gromacs/applied_forces/awh/pointstate.h (line 355)…
Huge Etotal difference between TIP4p implicit VS explicit methods from the manual script – LAMMPS Beginners
Have you read the manual: Yes. I used the scripts from Lammps manualMD simulation experience: Yes, several years, with Gromacs, Amber and OpenMMLammps experience: No. Started recentlyLammps version: 20230208Lammps execution command: mpirun -np xxx lmp -in in.tip4pCan you provide your input scripts and results: Yes. Please check this: Input scripts…
Solvation Energy calculation – User discussions
Teslim December 9, 2023, 1:49am 1 GROMACS version: 2020.2GROMACS modification: No I am trying to execute the free energy solvation calculation as described here “www.mdtutorials.com/gmx/free_energy/03_workflow.html”. In the job.sh file “www.mdtutorials.com/gmx/free_energy/Files/job.sh”, there is a loop from 0 to 20. the “init_lambda_state” in the mdp changes from 0 – 20. If I…
Diversity in minimal periodic distance in different 200-ns MD simulations – User discussions
GROMACS version: 2022.4GROMACS modification: Yes/No noHere post your questionDear GROMACS users I have completed a protein (WT & mutant) simulation for 200 ns in triplicates using Amber99sb force filed and TIP3P water model. I have used both cubic and dodecahedron boxes with a distance of 1.0 nm from the box…
Gromacs 2023.3 on Apple M3 chip – User discussions
GROMACS version: 2023.3GROMACS modification: No Hi folks I know that there have been several threads on running Gromacs with Apple M1 and M1 or M2 chips (e.g. Error compiling Gromacs 2023’s checks on Mac M2), but I recently got a MacBook Pro with the M3 chip, so I was interested…
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Installation error Gromacs 2023.3 – User discussions
GROMACS version:2023.3GROMACS modification: NoHere post your questionI am trying to install the Cuda version of Gromacs. However, I am getting the following error after executing cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=CUDA -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda. Error : [ 98%] Linking CXX executable …/…/…/bin/argon-forces-integration/bin/ld: /home/saikat/softwares/gromacs-2023.3/build/lib/libgromacs.so.8: undefined reference to srot_’ /bin/ld: /home/saikat/softwares/gromacs-2023.3/build/lib/libgromacs.so.8: undefined reference to strsm_’collect2:…
An error occurred in the pull code to implement the methane gas compression process under a certain – User discussions
Jiang December 8, 2023, 2:40pm 1 GROMACS version:2018.8GROMACS modification: Yes/NoHere post your questionHere is my code, I want to construct methane gas under certain temperature and pressure conditions by applying pressure to the graphene above, but I am not very clear about how to define the direction of stretching in…
Parallel run – User discussions
SP06 December 7, 2023, 4:28am 1 GROMACS version: 2021.4GROMACS modification:Here post your question : Can anyone please help me with how to run a parallel run on my Desktop. I went through the documentation for this but I could not understand it. Please explain how to do parallelization of the…
Charmm36-jul2022.ff – User discussions – GROMACS forums
GROMACS version:GROMACS modification: Yes/NoHere post your question I am trying to generate amylin 2L86.top using CHARMM36-jul2022.ff and TIP3P. Amylin has 37 residues but the last NH2 is considered as residue 38. Although AMBERsb-star-ILDN.ff works with 38 resiues”, Charmm36-jul2022 does not work (see below):Fatal error:Residue type ‘NH2’ not found in residue…
GROMACS MD Simulation – proteomics
I received this error when using the GROMACS initial setup tool WARNING: No ICDs were found. Either, Install a conda package providing a OpenCL implementation (pocl, oclgrind, intel-compute-runtime, beignet) or Make your system-wide implementation visible by installing ocl-icd-system conda package. jennaj December 7, 2023, 9:27pm 2 Hi @Vibha_Rao That is…
How to set awh1-dim1-diffusion and awh1-error-init properly – User discussions
Noob December 6, 2023, 9:13pm 1 GROMACS version: 2023.3GROMACS modification: NoI have been trying out the AWH accelerated sampling for gromacs to better sample the conformational space of a protein. I followed the AWH tutorial for gromacs using more or less the same mdp parameters just adjusted to fit my…
Gromacs distance calculation between multiple atoms, is it real? – User discussions
rufus December 6, 2023, 8:34pm 1 GROMACS version: 2022GROMACS modification: No Dear all, I have to analyze the trajectory and calculate all distances between a group of atoms (each separate one) and all the surrounding waters, which were at the distance cutoff < 0.35. There were times, when I used…
Atomtype not found but it is defined in forcefield files – User discussions
Wang December 5, 2023, 1:57pm 1 GROMACS version: 2019.4GROMACS modification: YesHi, I was trying to add ions to a protein mixture system using grompp but got an error concerning the top file stating that atomtype NH3 (referring to the first residue of the protein) was not found. However, NH3 as…
Gromacs geometry setup – User discussions
GROMACS version:2022_4GROMACS modification: Yes/NoI am relatively new to gromacs. I am trying to compare the dynamics of a solvated polymer in a confined geometry. (vertical rigid neutral interaction walls and lateral ceramic substrate) The three walls will interact with the polymer in a non-bonded interaction. I would like to group…
RMSD calculation error – User discussions
nhina December 5, 2023, 3:30am 1 GROMACS version: 2019GROMACS modification: Yes/NoHi All, My system contains protein, ligand and nowater. I want to calculate RMSD after simulation and i have used commands. gmx trjconv -s md_1.tpr -f md_1.xtc -o traj_1.xtc -pbc nojumpgmx rms -s md_1.tpr -f traj_1.xtc -o rmsd_noH_1.xvg -n Pro_MOL_noH.ndx…
Magic number – User discussions
Rochik December 5, 2023, 11:50am 1 GROMACS version: 2023Hello all,I finished a 1-micro-sec MD simulation, and I have 3 trajectories (because of some reasons the calculation stopped and I had to restart from the last point), now I need to concatenate the three trajectories by this command:gmx trjcat -f md_0_1.part0001.xtc…
Buckingham Potential in Recent Versions – User discussions
yehon December 4, 2023, 2:21pm 1 GROMACS version: 2021.5GROMACS modification: NoI am seeking advice on using the Buckingham potential in the latest versions of GROMACS, particularly with the Verlet integration scheme. My current version lacks support for the Buckingham potential under Verlet, and Group scheme isn’t an option either. Is…
Distance Restraints for Different Molecules – User discussions
yehon December 4, 2023, 10:03am 1 GROMACS version: 2021.5GROMACS modification: NoI am seeking guidance on implementing distance restraints in a system with multiple distinct molecules, as defined in the [molecules] section of the .itp file. Lets say my simulation involves a solution containing 20 molecules, and I wish to maintain…
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Improving MD Results Accuracy – User discussions
umar December 2, 2023, 1:32pm 1 GROMACS version: 2023.1GROMACS modification: No Hello. I run 100 ns MD of Ionic Liquids with GAFF.The value of density I got deviated by about 3 % from Experiment. Could one take a look at my production .mdp file and suggest some changes for improving…
Genion with alchemical transformations – User discussions
Hello GROMACS Community! I’m currently engaged in alchemical transformation simulations involving changes in net charge. I’m familiar with the challenges associated with charge changes and have been using the dual-system-in-a-single-box method to address them. However, during some test runs, I’ve come across a perplexing issue: In my test system, the…
Cross-linked polemer – User discussions
GROMACS version: 2019GROMACS modification: Yes/NoDear GROMACS people, I am working with a complex cross-linked polymer and need to calculate the interaction between this polymer and a protein using Gromacs software. I have obtained the force field parameters (OPLS-AA) and the polymer-related topology file using Schrödinger software, and I converted them…
GROMACS 2020 make error when installation – User discussions
jane_hi November 30, 2023, 9:57pm 1 Hi, I got an error when I install gromacs 2020 on windows subsystem of linuxThe scripts I ran are: wget [ftp.gromacs.org/gromacs/gromacs-2020.tar.gz] tar xfz gromacs-2020.tar.gz cd gromacs-2020/ mkdir build cd build/ sudo apt-get install -y fftw3 cmake … -DGMX_BUILD_OWN_FFTW=ON -DGMX_GPU=CUDA -DCMAKE_PREFIX_PATH=/home/GMX DGMX_FFT_LIBRARY=fftw3 -DCMAKE_C_COMPILER=gcc -DCMAKE_CXX_COMPILER=g++ make…
How to sample different maximum dimensions of a protein – User discussions
cjbraz December 1, 2023, 6:50am 1 GROMACS version: 2023.3GROMACS modification: Yes/NoHere post your question Hi all,I have run md simulations on a couple monomeric proteins. The results are promising but I am wanting to prompt the protein to sample at different maximum dimensions. For example, if the largest residue to…
High-Performance Computing Software Market Size [2023-2029] -Altair Engineering, Ansys, Dassault Systemes, ESI, Gaussian, Gro
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computational chemistry – How do you determine the Pull Direction for a GROMACS umbrella sampling simulation to generate the most accurate free energy value?
computational chemistry – How do you determine the Pull Direction for a GROMACS umbrella sampling simulation to generate the most accurate free energy value? – Matter Modeling Stack Exchange Stack Exchange Network Stack Exchange network consists of 183 Q&A communities including Stack Overflow, the largest, most trusted online community for…
who can share a package of gromacs-drude – User discussions
RogerM November 27, 2023, 8:07am 1 Recently, I wanted to run a polarizable simulation using gromacs with drude force filed. I got the install package using the command in MacKerell Lab, but it failed when I used “git clone . It shows the following error:fatal: unable to connect to git.gromacs.org:git.gromacs.org[0:…
Is it possible to move all atoms simultaneously in each timestep? – User discussions
Hi everyone, As you know, in MD simulation of a biological system, typically, one atom is moved in each timestep, followed by recalculating forced, then another atom is moved and so forth. Does GROMACS, or any other MD simulation tool such as NAMD, AMBER, etc., allows us to run the…
Error: Atomtype N3 not found while trying to obtain ions.tpr – User discussions
sam13 November 27, 2023, 12:33am 1 GROMACS version: 🙂 GROMACS – gmx grompp, 2023.3-Homebrew (-:GROMACS modification: No Hello,I have been trying to do MD simulation for a protein whose 3D structure is predicted by AlphaFold. The ligand is Aspartate molecule. I am following a similar approach to the Protein-Ligand GROMACS…
Best force field for miRNA simulations – User discussions
havlani November 25, 2023, 6:41am 1 GROMACS version: 2023.3-HomebrewGROMACS modification: NoHi all, I was wondering what is regarded as the best/most popular force field for dealing with miRNA (or RNA in general). I have read in this forum that the AMBER ones are quite outdated and should not be used,…
Shifts within periodic boundaries – User discussions
sd206 November 24, 2023, 8:15pm 1 GROMACS version:2023.2GROMACS modification: NoHello, I am running protein-protein complex with OPLS-AA force field in a cubic box. I got this error at the very first step of Energy minimization. How can I resolve the problem?Fatal error:There are inconsistent shifts over periodic boundaries in a…
ILVES, a new parallel constraint algorithm – Developers discussions
Lorien November 24, 2023, 12:27pm 1 Dear GROMACS developers, We are working on the development of a new parallel constraint algorithm named ILVES based on SHAKE’s equations. ILVES converges very rapidly, so our focus is to enable lower relative tolerances than the current default (shake-tol = 0.0001) with low performance…
Details of viscosity estimation (gmx energy -vis) – User discussions
GROMACS version: 2023.2GROMACS modification: No Hello everyone, I have started using gmx energy -vis to estimate shear viscosity (file visco.xvg) from equilibrium MD simulations. The command is very convenient and easy to use, but I would like to know the details of these calculations. For instance, it is not clear…
Hight pressure values in graphyne sheet – User discussions
GROMACS version: 2022GROMACS modification: no Hello everyone! I’m attempting to simulate a system that includes a graphyne sheet with water, K, and Cl ions at a concentration of 1 molar, under conditions of 300K and 1 bar pressure. The graphyne sheet was previously relaxed using DFT calculations. I acquired the…
Compiling Deep-md with GROMACS – User discussions
GROMACS version: 2020.2GROMACS modification: Yes/NoI was trying to install Deep-md with GROMACS following the link1.6. Install GROMACS with DeepMD — DeePMD-kit documentation. To do this, I have followed the link to install Deep-MD: 1.2. Install from source code — DeePMD-kit documentationHere I have successfully completed the 1.2.1 ( install-the-python-interface) and…
Creating a .pdb file from .cml file – User discussions
jankac November 23, 2023, 11:32am 1 GROMACS version: 2023.3GROMACS modification: NoHi everyone!I’m really new to the gromacs and I’m trying to create my first input. The molecule I want to use is a peptide I’m researching. I created a model of my molecule in Avogadro and then converted it to…
How to do the MD simulation of a metalloenzyme with ligand? – User discussions
GROMACS version: 2023GROMACS modification: YesHere post your question : Recently, I want to make the simulation of a metalloenzyme with ligand. The metalloenzyme has two Mn ions in its active site. When producing the topol file for this metalloenzyme, gromacs cannot find the Mn ion in the rtp file. I…
Small rigid molecules with constraints – User discussions
tnagai November 22, 2023, 1:47pm 1 GROMACS version: 2023.1GROMACS modification: No I modelled a small rigid-body nitrate ion (or NO3+) with 6 constraints.However, I observed weird and large oscillations during a simulation with LINCS (and many errors). It seems (at least visually) fine or OK with SHAKE.Could you please let…
Is it important to repeat analysis – User discussions
pelinsu November 22, 2023, 7:27pm 1 GROMACS version:GROMACS modification: Yes/NoHere post your questionIs it important to repeat the simulation? My RMSD values are quite good and the VMD movie is successful. Extra SASA, RMSF, protein-ligand interaction analysis was performed. But is it still important to do 3 repetitions? for publication…
Problem with PYTORCH & LIBTORCH
Hi I tried to run a run using a deepLDA model, but it gives me the following error: PLUMED: ERROR PLUMED: (core/PlumedMain.cpp:823) void PLMD::PlumedMain::readInputWords(const std::vector<std::__cxx11::basic_string<char> >&)PLUMED: I cannot understand line: PYTORCH_MODEL LABEL=s FILE=deepLDA_4efu_1try.ptc ARG=D_cL1w,D_cL2w,D_cL3w,D_cBw,D_cE1w,D_cE2w,D_cE3w,D_cvw1,D_cvw2,D_cvw3,D_cvw4,D_cvw5,D_cvw6,D_cvw7,D_cvw8,D_cvw9,D_cvw10,D_cvw11,D_cvw12,D_cvw13,D_cvw14,D_cvw15,D_cvw16,D_cvw17,D_cvw18,D_cvw19,D_cvw20,D_d1A,D_d2A,D_d3A,D_d4A,D_d5A,D_d6A,D_d7A,D_d8A,D_d9A,D_d10A,D_d11A,D_d12A,D_d13A,D_d1B,D_d2B,D_d3B,D_d4B,D_d5B,D_d6B,D_d7B,D_d8B,D_d9B,D_d10B,D_d11B,D_d12B,D_d13BPLUMED: Maybe a missing space or a typo? ################################################################################ I checked the pytorch and libtorch modules and noticed…
Running GROMACS efficiently on LUMI workshop 2024
Registration for BioExcel’s workshop on How to run GROMACS efficiently on the LUMI supercomputer is now open. This course gives practical tips on how to run GROMACS simulations efficiently on LUMI-G, i.e., on AMD GPUs. The participants will learn how to assess and tune GROMACS performance. In addition, the course provides…
Possible inclusion of PLUMED interface – Developers discussions
Dear GROMACS developers, we (PLUMED developers) noticed that GROMACS now makes it possible to easily add plugins modifying forces. We would like to investigate if it makes sense for us to implement an interface for PLUMED in the spirit of the one introduced for the Colvars package in this commit:…
Forcefield recommendations for protein-ligand system – User discussions
Panuwid November 21, 2023, 4:44pm 1 GROMACS version:2023.2-HomebrewGROMACS modification: Yes/NoHere post your questionI am studying a small protein and a small molecule . I have found that there are many forcefields that can be used for protein-ligand studies, but I am not sure which one is the best fit for…
GROMACS 2024 beta release – Developers discussions
Dear GROMACS Developers, The 2024-beta has just been released, see the announcement below: Hi, GROMACS users! The beta release of GROMACS 2024 is available! We are making this available to you to get an early taste of how GROMACS 2024 will look and work, and most importantly to get feedback…
Changes in input parameter files – User discussions
SP06 November 20, 2023, 6:19am 1 GROMACS version: 2021GROMACS modification: Yes/NoHere post your question : In the gromacs tutorials page for a protein in water, in the input parameter files from energy minimization to npt equilibration steps, its given for 100 ps and for the production run it’s given for…
How to solve the GROMACS error “One or more water molecules can not be settled” during SMD? – User discussions
mari November 19, 2023, 6:17pm 1 GROMACS version:2019.6GROMACS modification: NoHow to solve the GROMACS error “One or more water molecules can not be settled” during SMD?I hope this message finds you well. I’m currently conducting research involving simulating a membrane protein system using GROMACS 2019.6. I have encountered an issue…
Error installation GPU OPENCL gromacs, Please help – User discussions
i get this error when i install gromacsben@ben-System-Product-Name:~/gromacs-2023.3/build$ cmake … -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON– GPU support with OpenCL is deprecated. It is still fully supported (and recommended for AMD, Intel, and Apple GPUs). It may be replaced by different approaches in future releases of GROMACS.CMake Error at cmake/gmxManageOpenCL.cmake:51 (message):OpenCL is not supported….
Colvar module with GROMACS does not work – User discussions
GROMACS version: 2022.5GROMACS modification: NoHere post your question Dear GROMACS community, I need to perform umbrella sampling simulations. For generation of the umbrella sampling windows, I would like to use the “colvars” module, which, according to the documentation (colvars.github.io/master/colvars-refman-gromacs.pdf)), can be used in gromacs. Following the procedures described in this…
Gmx trjconv giving trajectory file with zero values in y and z coordinates – User discussions
GROMACS version: 2021.1GROMACS modification: Yes/NoDear colleagues,I have done clustering with 1,2- hexanediol molecule using gmx cluster and got a index file out put from cluster frames. Using that index file when I am extracting the cluster members as a trajectory using trajcov I am getting the output file but it…
Gmx trjconv -fit – User discussions
Lili November 16, 2023, 8:00pm 1 Program: gmx trjconv, version 2021.3-MODIFIEDSource file: src/gromacs/pbcutil/pbc.cpp (line 101)Function: numPbcDimensions(PbcType)::<lambda()>Hi,I am preparing gmx_MMPBSA calculations after production mdrun,Bellow are my two commands. I first command survive but the second give errores as I pasted bellow.Command 1:gmx trjconv -s topol.tpr -f traj.xtc -o md_noPBC_center.xtc -pbc atom…
University Positions – Postdoc in GPU algorithms for molecular dynamics with GROMACS
Job description We are looking for an HPC expert to contribute to one or multiple projects related to the GROMACS molecular simulation software. GROMACS is one of the most important HPC applications in the world and runs on all modern CPU and GPU architectures. GROMACS uses a hierarchical parallelization with…
Segmentation fault when running an NPT – User discussions
GROMACS version: 2023.2GROMACS modification: Yes/No Hello and good day, I am running some cycles of NVT-NPT for swelling procedures on a membrane. Each cycle goes like this NVT for 250 ps with T goes from 300-600 CNVT for 500 ps with T at 600 CNVT for 250 ps with T…
Recreate P(Wf) & P(-Wr) from the raw data – User discussions
pinoji1 November 16, 2023, 10:16pm 1 GROMACS version:2023.3GROMACS modification: No“Can I recreate P(Wf) & P(-Wr) by myself from the raw data?”When I originally run the alchemical simulation (solute, solvent ,and ions), I get dgdl.xvg file for nonequilibium free energy calculations from a starting state A (I just choose the first…
Simulated ligand with weird geometries on start.pdb(dump=0) and md_0_100.gro files – User discussions
GROMACS version:2021.4-UbuntuGROMACS modification: Yes/NoHere post your question: I run 100nsec simulation with all ‘default’ parameter suggested by the tutorial Protein-Ligand Complex. After 10 days the simulation was finally over. To visualize the results prior to the analysis step, i uploaded into Pymol start.pdb(dump0) and md_0_100.gro. What I saw was that…
Correcting non integral charge on ligand – User discussions
GROMACS version: 2020.4GROMACS modification: No Dear all, I was trying to simulate a protein ligand complex in Gromacs 2020.4, using OPLSAAff. the parameters for ligand was generated using the server LigParGen. The total charge on the ligand sums up to 0.0002, how to deal with this?I checked for any floating…
Nvidia announces H200, designed to handle AI work better, How better is it than the H100? Know here
Nvidia H200: Leading chip manufacturer Nvidia has released the H200, a top-of-the-line chipset designed for AI applications. With numerous large firms, including Amazon Web Services, Google Cloud, Microsoft Azure, and Oracle Cloud Infrastructure, already pledging to utilise the chipset next year, the upgrade to the already well-liked H100 chipset will begin…
Are these timings fine? – User discussions
lutek14 November 14, 2023, 7:02am 1 GROMACS version: gromacs/2021.4_mpi_plumedGROMACS modification: No Hello,I am running Gromacs on HPC for the first time, and I am unsure if the timings are fine. I am not sure whether I have allocated too many or too few resources. The system consists of 57,810 atoms.The…
How do I print out the energy of solute from edr file? – User discussions
pinoji1 November 14, 2023, 8:35pm 1 GROMACS version:2023.3GROMACS modification: NoHow do I print out the energy of solute during the production run in alchemical transformation? I triedgmx energy -f myfile.edr -n myfile.ndx -o solE.xvgBut -n option is not available. Is there any other way to access this information during alchemical…
Inhibition of providencia vermicola FabD
Introduction Microbial resistance has become a problem in the contemporary medical environment due to the inadequate development of new antibiotics and the asinine prescription of antibiotics in both developed and developing nations. Antimicrobial resistance (AMR), which affects wealthy and developing nations, is a global concern.1 AMR is a problem for…