# MDWeb **URL:** https://ask.bioexcel.eu/c/mdweb/11.md [Latest](https://ask.bioexcel.eu/latest.md) · [Categories](https://ask.bioexcel.eu/categories.md) · [Tags](https://ask.bioexcel.eu/tags.md) --- ## [About the MDWeb category](https://ask.bioexcel.eu/t/about-the-mdweb-category/114)
**Author:** [@adamepcc](https://ask.bioexcel.eu/u/adamepcc)\ **Replies:** 4\ **Last updated:** [April 3, 2019, 2:37pm UTC](https://ask.bioexcel.eu/t/about-the-mdweb-category/114 "2019-04-03T14:37:29Z")
MDWeb - Molecular dynamics on the web provides a web interface to set up molecular dynamics simulations at https://mmb.irbbarcelona.org/MDWeb/ --- ## [Can't log in after registration](https://ask.bioexcel.eu/t/cant-log-in-after-registration/5589)
**Author:** [@zyzhang](https://ask.bioexcel.eu/u/zyzhang)\ **Replies:** 1\ **Last updated:** [April 14, 2025, 7:20am UTC](https://ask.bioexcel.eu/t/cant-log-in-after-registration/5589 "2025-04-14T07:20:18Z")
Hi all, I can’t log in MDWeb after registration. Help me please… --- ## [MDWeb problem: "maximum number of atoms"](https://ask.bioexcel.eu/t/mdweb-problem-maximum-number-of-atoms/5223)
**Author:** [@smar96](https://ask.bioexcel.eu/u/smar96)\ **Replies:** 3\ **Last updated:** [August 21, 2024, 11:00am UTC](https://ask.bioexcel.eu/t/mdweb-problem-maximum-number-of-atoms/5223 "2024-08-21T11:00:28Z")
Hello, I am trying to create a new project for (PDB 4oie) and the system does not allow me, incorrectly reporting: “PDB file exceeds maximum number of Atoms (20000)”. This is not true, the raw PDB has 1551 atoms (inclu… --- ## [Trajectory snapshot](https://ask.bioexcel.eu/t/trajectory-snapshot/3766)
**Author:** [@leilasu](https://ask.bioexcel.eu/u/leilasu)\ **Replies:** 4\ **Last updated:** [February 15, 2024, 1:18am UTC](https://ask.bioexcel.eu/t/trajectory-snapshot/3766 "2024-02-15T01:18:08Z")
Hello, it seems all the trajectory snapshot structure downloaded are the same, either by get a trajectory snapshot or by get a trajectory fragment operation. Can I get structure of a particular snapshot, like #500? Thank… --- ## [Problem with uploaded pdb file in Create Project](https://ask.bioexcel.eu/t/problem-with-uploaded-pdb-file-in-create-project/4837)
**Author:** [@leilasu](https://ask.bioexcel.eu/u/leilasu)\ **Replies:** 0\ **Last updated:** [February 15, 2024, 1:10am UTC](https://ask.bioexcel.eu/t/problem-with-uploaded-pdb-file-in-create-project/4837 "2024-02-15T01:10:47Z")
Hi Adam, I got the error messages below when I “Create Project” with an uploaded pdb file. This structure file had been used before without any problem. I am wondering what is the issue here. Thanks!! - leila Warning :… --- ## [Out of memory issue while using MDweb GROMACS simulation](https://ask.bioexcel.eu/t/out-of-memory-issue-while-using-mdweb-gromacs-simulation/4731)
**Author:** [@SJLee](https://ask.bioexcel.eu/u/SJLee)\ **Replies:** 3\ **Last updated:** [January 5, 2024, 10:19am UTC](https://ask.bioexcel.eu/t/out-of-memory-issue-while-using-mdweb-gromacs-simulation/4731 "2024-01-05T10:19:11Z")
Thank you for the amazing program Input pdb file was a receptor and a vaccine ligand complex of 1796 amino acids in total After full MD setup for GROMACS, I ran it with NPT option but it gives me an error as the one b… --- ## [Workflow still queued, waiting for a free processor to run](https://ask.bioexcel.eu/t/workflow-still-queued-waiting-for-a-free-processor-to-run/4753)
**Author:** [@Zikc](https://ask.bioexcel.eu/u/Zikc)\ **Replies:** 1\ **Last updated:** [January 5, 2024, 10:07am UTC](https://ask.bioexcel.eu/t/workflow-still-queued-waiting-for-a-free-processor-to-run/4753 "2024-01-05T10:07:51Z")
When I make the Base Structure, when I select the force field for processing, it always shows the Progress info, Workflow still queued, waiting for a free processor to run… --- ## [Problem running gromacs simulation](https://ask.bioexcel.eu/t/problem-running-gromacs-simulation/4620)
**Author:** [@sajjadnej](https://ask.bioexcel.eu/u/sajjadnej)\ **Replies:** 27\ **Last updated:** [November 14, 2023, 2:21pm UTC](https://ask.bioexcel.eu/t/problem-running-gromacs-simulation/4620 "2023-11-14T14:21:22Z")
Hi, I used your server to generate config files for gromacs md simulation with amber99sb\* forcefield. I also wanted to upload and submit these files that your server generate in GRIDMARKETS gromacs. but their server enc… --- ## [GROMACS NPT simulation error after running for 3-4 days](https://ask.bioexcel.eu/t/gromacs-npt-simulation-error-after-running-for-3-4-days/3970)
**Author:** [@DimChem13](https://ask.bioexcel.eu/u/DimChem13)\ **Replies:** 3\ **Last updated:** [November 14, 2022, 8:07am UTC](https://ask.bioexcel.eu/t/gromacs-npt-simulation-error-after-running-for-3-4-days/3970 "2022-11-14T08:07:45Z")
Dear MDWeb, I had set up a GROMACS NPT simulation and it was running for 3-4 days but never finished. Instead, it gave me the error sign. When I checked the log file it gave a massive list but I dont seem to be able to … --- ## ["Analysis tools" processes never finish](https://ask.bioexcel.eu/t/analysis-tools-processes-never-finish/3962)
**Author:** [@DimChem13](https://ask.bioexcel.eu/u/DimChem13)\ **Replies:** 1\ **Last updated:** [October 27, 2022, 9:09am UTC](https://ask.bioexcel.eu/t/analysis-tools-processes-never-finish/3962 "2022-10-27T09:09:33Z")
Hello, I’ve run 5 Gromacs FULL MD setups and wanted to use some Analysis tools (“RMSd per residue”, “Average structure”) but all these processes keep on running for 2 days without any results. Have I done something … --- ## [Protein-peptide ligand MD](https://ask.bioexcel.eu/t/protein-peptide-ligand-md/3952)
**Author:** [@DimChem13](https://ask.bioexcel.eu/u/DimChem13)\ **Replies:** 0\ **Last updated:** [October 20, 2022, 3:54pm UTC](https://ask.bioexcel.eu/t/protein-peptide-ligand-md/3952 "2022-10-20T15:54:54Z")
Hello, I would like to perform MD of a peptide ligand with a protein using MDWeb but I am a bit confused on some step and I would like to kindly ask for some help. If the pdb file of the protein I want to use only exis… --- ## [Error loading trajectory, check topology and trajectory matching and accordance with formats selected](https://ask.bioexcel.eu/t/error-loading-trajectory-check-topology-and-trajectory-matching-and-accordance-with-formats-selected/3786)
**Author:** [@christos-efthymiou](https://ask.bioexcel.eu/u/christos-efthymiou)\ **Replies:** 6\ **Last updated:** [July 1, 2022, 7:05am UTC](https://ask.bioexcel.eu/t/error-loading-trajectory-check-topology-and-trajectory-matching-and-accordance-with-formats-selected/3786 "2022-07-01T07:05:04Z")
I would like to use MDWeb to analyze some molecular dynamics simulations, but I when I try to upload my trajectory and topology file, I get the following error: Error loading trajectory, check topology and trajectory ma… --- ## [Is MDWEB working?](https://ask.bioexcel.eu/t/is-mdweb-working/2834)
**Author:** [@s8nasing](https://ask.bioexcel.eu/u/s8nasing)\ **Replies:** 4\ **Last updated:** [June 16, 2022, 6:33pm UTC](https://ask.bioexcel.eu/t/is-mdweb-working/2834 "2022-06-16T18:33:08Z")
Hii, I am trying to generate the simulation files by running NAMD full setup but It’s showing “workflow in queue waiting for free processor”. The thing is I have submittied the job on 1st march, it’s already been 5 days… --- ## [Need help following Protein Analysis Tutorial](https://ask.bioexcel.eu/t/need-help-following-protein-analysis-tutorial/3272)
**Author:** [@chaitsunthai](https://ask.bioexcel.eu/u/chaitsunthai)\ **Replies:** 4\ **Last updated:** [September 29, 2021, 9:00am UTC](https://ask.bioexcel.eu/t/need-help-following-protein-analysis-tutorial/3272 "2021-09-29T09:00:04Z")
Dear Adam, Thanks for making MDWeb available. Such an excellent service to the research community! I am now trying to learn it so that I can use it to generate a RMSd plot for my docked compound.(Please forgive me if m… --- ## [MDweb server couldn't able to run nvt and npt](https://ask.bioexcel.eu/t/mdweb-server-couldnt-able-to-run-nvt-and-npt/3226)
**Author:** [@ummul](https://ask.bioexcel.eu/u/ummul)\ **Replies:** 2\ **Last updated:** [August 30, 2021, 5:57am UTC](https://ask.bioexcel.eu/t/mdweb-server-couldnt-able-to-run-nvt-and-npt/3226 "2021-08-30T05:57:36Z")
hello, i am trying to run molecular dynamics throug MDweb server , i succesfully generated the files for md set up using Gromacs MD full set up, i am trying to generate nvt and npt but i couldn’t successfully run… how to… --- ## [GROMACS Full MD Setup error](https://ask.bioexcel.eu/t/gromacs-full-md-setup-error/3145)
**Author:** [@vdvornyk](https://ask.bioexcel.eu/u/vdvornyk)\ **Replies:** 1\ **Last updated:** [August 28, 2021, 8:34am UTC](https://ask.bioexcel.eu/t/gromacs-full-md-setup-error/3145 "2021-08-28T08:34:49Z")
Hello, During the setup, the following error is generated: Option Filename Type Description -f 5\_162509376014205.gromacs.mdp Input, Opt! grompp input file with MD parameters -po mdout.mdp Output grompp input file wit… --- ## [MDWeb is reporting java runtime environment failure](https://ask.bioexcel.eu/t/mdweb-is-reporting-java-runtime-environment-failure/2889)
**Author:** [@SharonJXY](https://ask.bioexcel.eu/u/SharonJXY)\ **Replies:** 2\ **Last updated:** [April 15, 2021, 1:21pm UTC](https://ask.bioexcel.eu/t/mdweb-is-reporting-java-runtime-environment-failure/2889 "2021-04-15T13:21:53Z")
Hi, I am pretty sure I have my Java Runtime Environment update to the latest and enabled Java applet in my browser. But the protein visualization does not work. I have asked several friends to try MDWeb on different pla… --- ## [Unknown pdb or swiss-prot code](https://ask.bioexcel.eu/t/unknown-pdb-or-swiss-prot-code/2850)
**Author:** [@nabil](https://ask.bioexcel.eu/u/nabil)\ **Replies:** 5\ **Last updated:** [March 17, 2021, 8:24am UTC](https://ask.bioexcel.eu/t/unknown-pdb-or-swiss-prot-code/2850 "2021-03-17T08:24:34Z")
hi everyone, when i try to upload a pdb file from my pc to start a new project, i obtain this error : unknown pdb or swiss prot code . im sure for the pdb structure --- ## [Is MDWeb working?](https://ask.bioexcel.eu/t/is-mdweb-working/2629)
**Author:** [@lavionia256](https://ask.bioexcel.eu/u/lavionia256)\ **Replies:** 3\ **Last updated:** [February 19, 2021, 8:07am UTC](https://ask.bioexcel.eu/t/is-mdweb-working/2629 "2021-02-19T08:07:59Z")
Hi! A few days ago I performed some simulations on MDWeb. Then I tried to repeat the process in different temperature, from the same setup files - and I’ve received an error (the simulation started, kept going for a day… --- ## [Error at neutralizing step](https://ask.bioexcel.eu/t/error-at-neutralizing-step/2792)
**Author:** [@Gayatri](https://ask.bioexcel.eu/u/Gayatri)\ **Replies:** 1\ **Last updated:** [January 25, 2021, 9:45pm UTC](https://ask.bioexcel.eu/t/error-at-neutralizing-step/2792 "2021-01-25T21:45:01Z")
Hi, I have been trying to run AMBER FULL MD SETUP, but getting stuck/ getting an error at the neutralizing step. My protein is neutral. How do I go ahead? please guide. --- ## [Temperature and pressure control](https://ask.bioexcel.eu/t/temperature-and-pressure-control/2696)
**Author:** [@alves.chem](https://ask.bioexcel.eu/u/alves.chem)\ **Replies:** 1\ **Last updated:** [December 7, 2020, 10:01am UTC](https://ask.bioexcel.eu/t/temperature-and-pressure-control/2696 "2020-12-07T10:01:07Z")
My question is regarding the simultaneous control of temperature and pressure. (a) To control the temperature a re-scale of particle velocities is needed and, (b) To control the pressure the volume (particle positons) … --- ## [Limited Molecular Dynamics Simulation Time](https://ask.bioexcel.eu/t/limited-molecular-dynamics-simulation-time/2415)
**Author:** [@pk\_20](https://ask.bioexcel.eu/u/pk_20)\ **Replies:** 7\ **Last updated:** [August 30, 2020, 7:32pm UTC](https://ask.bioexcel.eu/t/limited-molecular-dynamics-simulation-time/2415 "2020-08-30T19:32:57Z")
Is there any way so that we can set the simulation time for a production run manually? For example, is it possible for me to run a simulation (production) for atleast 20000 ps? If yes, then how? --- ## [Binding Constant Determination](https://ask.bioexcel.eu/t/binding-constant-determination/2386)
**Author:** [@mayks1996](https://ask.bioexcel.eu/u/mayks1996)\ **Replies:** 1\ **Last updated:** [August 13, 2020, 6:19pm UTC](https://ask.bioexcel.eu/t/binding-constant-determination/2386 "2020-08-13T18:19:08Z")
Hello, I am just starting to learn how to use the MDWeb simulations on the website. I was wondering if anyone may provide insights upon how to set up a run. I am looking to simulate the binding interactions between a pe… --- ## [Generated .pdb file not getting uploaded](https://ask.bioexcel.eu/t/generated-pdb-file-not-getting-uploaded/2372)
**Author:** [@seema](https://ask.bioexcel.eu/u/seema)\ **Replies:** 1\ **Last updated:** [August 2, 2020, 7:22am UTC](https://ask.bioexcel.eu/t/generated-pdb-file-not-getting-uploaded/2372 "2020-08-02T07:22:33Z")
Structure file generated at my end, Is in proper .pdb format with a Header, a Reamrk and ATOM field, still it is showing an error getting uploaded! It is properly recognized by other softwares. --- ## [Confusion regarding force field](https://ask.bioexcel.eu/t/confusion-regarding-force-field/2318)
**Author:** [@Anurabh](https://ask.bioexcel.eu/u/Anurabh)\ **Replies:** 1\ **Last updated:** [July 12, 2020, 2:43pm UTC](https://ask.bioexcel.eu/t/confusion-regarding-force-field/2318 "2020-07-12T14:43:19Z")
Are “AMBER99SB\*” and “AMBER99SB\*-ILDN” the same force field? If they are different can someone point me to the relevant publications describing them. Thanks in advance. --- ## [Ligands discarded](https://ask.bioexcel.eu/t/ligands-discarded/2303)
**Author:** [@help\_me](https://ask.bioexcel.eu/u/help_me)\ **Replies:** 1\ **Last updated:** [July 9, 2020, 12:10pm UTC](https://ask.bioexcel.eu/t/ligands-discarded/2303 "2020-07-09T12:10:23Z")
Hi I am facing an error with the structure I’ve uploaded. Despite uploading .lib and .frcmod files, my ligand is getting discarded. I have a phosphotyrosine in my structure, and as recommended for AMBER full MD setup, … --- ## [Expected amount of time required for running a MD Simulation](https://ask.bioexcel.eu/t/expected-amount-of-time-required-for-running-a-md-simulation/2008)
**Author:** [@Anurabh](https://ask.bioexcel.eu/u/Anurabh)\ **Replies:** 2\ **Last updated:** [May 11, 2020, 11:43am UTC](https://ask.bioexcel.eu/t/expected-amount-of-time-required-for-running-a-md-simulation/2008 "2020-05-11T11:43:22Z")
The file size hasn’t changed for the last 4 hours, is something wrong. --- ## [About seed for simulation](https://ask.bioexcel.eu/t/about-seed-for-simulation/1854)
**Author:** [@matsuzawa](https://ask.bioexcel.eu/u/matsuzawa)\ **Replies:** 1\ **Last updated:** [March 13, 2020, 10:19am UTC](https://ask.bioexcel.eu/t/about-seed-for-simulation/1854 "2020-03-13T10:19:54Z")
Hello. I created new project, and prepared for simulation by “Gromacs FULL MD setup”. Using this prepared structure, I ran “Simple Box Solvent Molecular Dynamics (NPT)” 2 times. After simulation, I noticed that these … --- ## [Stuck at "minimizing hydrogens"](https://ask.bioexcel.eu/t/stuck-at-minimizing-hydrogens/1840)
**Author:** [@MikaelW](https://ask.bioexcel.eu/u/MikaelW)\ **Replies:** 1\ **Last updated:** [March 2, 2020, 10:32am UTC](https://ask.bioexcel.eu/t/stuck-at-minimizing-hydrogens/1840 "2020-03-02T10:32:25Z")
First of all a huge thanks for such a nice and intuitive tool! My first few preparations and runs went smooth, but now whenever I try to prepare a protein for either Gromacs- or NAMD MD, the service gets stuck at the “m… --- ## [Downloading Energy Parameters, Hydrogen Bond Info, and SSE](https://ask.bioexcel.eu/t/downloading-energy-parameters-hydrogen-bond-info-and-sse/1715)
**Author:** [@skhan21](https://ask.bioexcel.eu/u/skhan21)\ **Replies:** 1\ **Last updated:** [October 10, 2019, 4:00pm UTC](https://ask.bioexcel.eu/t/downloading-energy-parameters-hydrogen-bond-info-and-sse/1715 "2019-10-10T16:00:45Z")
Hi, I am looking for a way to download the energy parameters for MD simulations that I have run on MDWeb. Also, is it possible to download information on the number of intra-molecular hydrogen bonds or secondary structu… [Next page](https://ask.bioexcel.eu/c/mdweb/11.md?page=1)