# Problem running gromacs simulation **URL:** \ **Category:** MDWeb\ **Created:** [October 20, 2023, 2:27pm UTC](https://ask.bioexcel.eu/t/problem-running-gromacs-simulation/4620 "2023-10-20T14:27:35Z")\ **Posts on this page:** 20\ **Page:** 1
**Author:** ![sajjadnej](https://avatars.discourse-cdn.com/v4/letter/s/e274bd/32.png) [@sajjadnej](https://ask.bioexcel.eu/u/sajjadnej)\ **Post date:** [October 20, 2023, 2:27pm UTC](https://ask.bioexcel.eu/t/problem-running-gromacs-simulation/4620/1 "2023-10-20T14:27:35Z")
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 encountered a problem that is: you’ll see from the log that your 1\_169770198911976.top topology files includes a reference to a “ffamber99sbstar.itp” that wasn’t included in your submission ---
**Author:** ![adam.hospital](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/adam.hospital/32/151_2.png) [@adam.hospital](https://ask.bioexcel.eu/u/adam.hospital)\ **Post date:** [October 23, 2023, 11:09am UTC](https://ask.bioexcel.eu/t/problem-running-gromacs-simulation/4620/2 "2023-10-23T11:09:05Z")
Hi, find attached the GROMACS force-fields included in MDWeb server, were you can find the ffamber99sbstar.itp file. Please note that MDWeb is a very old platform (using GROMACS v4). I strongly recommend you to use new platforms such as [BioBB](https://mmb.irbbarcelona.org/biobb/), through the [Jupyter Notebooks](https://mmb.irbbarcelona.org/biobb/workflows) or the [BioBB\_Wfs Web interface](https://mmb.irbbarcelona.org/biobb-wfs/) (much similar to MDWeb). Thanks for using our tools! [MDWeb\_GMX\_ffs.tgz.txt](https://ask.bioexcel.eu/uploads/short-url/128cyZRMxZC1wMNEfo6B0eRTBpX.txt) (2.3 MB) ---
**Author:** ![sajjadnej](https://avatars.discourse-cdn.com/v4/letter/s/e274bd/32.png) [@sajjadnej](https://ask.bioexcel.eu/u/sajjadnej)\ **Post date:** [October 26, 2023, 7:52am UTC](https://ask.bioexcel.eu/t/problem-running-gromacs-simulation/4620/3 "2023-10-26T07:52:42Z")
Thank you for your response. I have a problem after running the job. It can’t clone the job. What should I do? Thanks ![Caxpture.JPG](https://europe1.discourse-cdn.com/flex013/uploads/bioexcel/original/1X/3f4a41115f6491d430336aca6c92644ba4103c03.jpeg) ---
**Author:** ![sajjadnej](https://avatars.discourse-cdn.com/v4/letter/s/e274bd/32.png) [@sajjadnej](https://ask.bioexcel.eu/u/sajjadnej)\ **Post date:** [October 26, 2023, 8:34am UTC](https://ask.bioexcel.eu/t/problem-running-gromacs-simulation/4620/4 "2023-10-26T08:34:56Z")
I also have a question. How can I run the project on my own computer with gromacs? I mean in your old website there was a option that you could download the configuration for gromacs setup with .itp .tpr and other formats needed. ---
**Author:** ![adam.hospital](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/adam.hospital/32/151_2.png) [@adam.hospital](https://ask.bioexcel.eu/u/adam.hospital)\ **Post date:** [October 26, 2023, 8:43am UTC](https://ask.bioexcel.eu/t/problem-running-gromacs-simulation/4620/5 "2023-10-26T08:43:35Z")
Hi, we are trying to reproduce your problem with the project cloning, in our case is working fine. Can you tell us the project ID? And also why do you need to clone the project? To run the production simulation with GROMACS in your computer, please take a look at the help pages: > **[Help - BioExcel Building Blocks Workflows](https://mmb.irbbarcelona.org/biobb-wfs/help/workflows-home/gmx-prod)** > > Help page for BioExcel Building Blocks Workflows You can actually also run the setup workflow in your computer: > **[Help - BioExcel Building Blocks Workflows](https://mmb.irbbarcelona.org/biobb-wfs/help/workflows-home/python)** > > Help page for BioExcel Building Blocks Workflows ---
**Author:** ![sajjadnej](https://avatars.discourse-cdn.com/v4/letter/s/e274bd/32.png) [@sajjadnej](https://ask.bioexcel.eu/u/sajjadnej)\ **Post date:** [October 26, 2023, 8:49am UTC](https://ask.bioexcel.eu/t/problem-running-gromacs-simulation/4620/6 "2023-10-26T08:49:30Z")
Thank you for you response. I could clone it. I thought I should clone it for running with personal computer. Now you say that I dont need to clone the project. ---
**Author:** ![sajjadnej](https://avatars.discourse-cdn.com/v4/letter/s/e274bd/32.png) [@sajjadnej](https://ask.bioexcel.eu/u/sajjadnej)\ **Post date:** [October 26, 2023, 9:05am UTC](https://ask.bioexcel.eu/t/problem-running-gromacs-simulation/4620/7 "2023-10-26T09:05:08Z")
also I dont get this in help section. In this case, the **GROMACS portable binary file (tpr)** needed for GROMACS to run a **production MD** has been generated. how should i generate tpr file? ---
**Author:** ![sajjadnej](https://avatars.discourse-cdn.com/v4/letter/s/e274bd/32.png) [@sajjadnej](https://ask.bioexcel.eu/u/sajjadnej)\ **Post date:** [October 26, 2023, 9:13am UTC](https://ask.bioexcel.eu/t/problem-running-gromacs-simulation/4620/8 "2023-10-26T09:13:46Z")
and another question. The old server provided files with .tpr .top .gro and .mdp formats to run gromacs. Is there an option to do this with the new server? ![Captur2e](https://europe1.discourse-cdn.com/flex013/uploads/bioexcel/original/1X/a5a562977bb8720add964868da490d3aa745786f.jpeg) ---
**Author:** ![adam.hospital](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/adam.hospital/32/151_2.png) [@adam.hospital](https://ask.bioexcel.eu/u/adam.hospital)\ **Post date:** [October 26, 2023, 9:21am UTC](https://ask.bioexcel.eu/t/problem-running-gromacs-simulation/4620/9 "2023-10-26T09:21:27Z")
Hi, the tpr file for the production run can be generated checking the corresponding option in the GROMACS setup workflow inputs: ![image](https://europe1.discourse-cdn.com/flex013/uploads/bioexcel/original/1X/4f1b9fcbc5da57dd616b012f2cfc2d29d02fa1f9.png) the files you ask for will be then included in the output files to download: ![image](https://europe1.discourse-cdn.com/flex013/uploads/bioexcel/original/1X/f52a0aebbb2aa57e2ef63c9bee2052916a94b47e.png) All of these options are explained in the help pages. Hope it helps! ---
**Author:** ![sajjadnej](https://avatars.discourse-cdn.com/v4/letter/s/e274bd/32.png) [@sajjadnej](https://ask.bioexcel.eu/u/sajjadnej)\ **Post date:** [October 26, 2023, 9:35am UTC](https://ask.bioexcel.eu/t/problem-running-gromacs-simulation/4620/10 "2023-10-26T09:35:46Z")
Thank you very much for your continued support. ---
**Author:** ![sajjadnej](https://avatars.discourse-cdn.com/v4/letter/s/e274bd/32.png) [@sajjadnej](https://ask.bioexcel.eu/u/sajjadnej)\ **Post date:** [October 26, 2023, 9:46am UTC](https://ask.bioexcel.eu/t/problem-running-gromacs-simulation/4620/11 "2023-10-26T09:46:57Z")
sorry for bothering you again. In the output file there is no .mdp file for gromacs setup. what should i do? ---
**Author:** ![adam.hospital](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/adam.hospital/32/151_2.png) [@adam.hospital](https://ask.bioexcel.eu/u/adam.hospital)\ **Post date:** [October 26, 2023, 10:13am UTC](https://ask.bioexcel.eu/t/problem-running-gromacs-simulation/4620/12 "2023-10-26T10:13:02Z")
Hi, the server is generating the tpr for you so you don’t need the mdp file anymore, unless you want to generate your own tpr file. In this case, is up to you to generate your own mdp file with the desired gromacs parameters. You can start with the [official gromacs mdp template](https://manual.gromacs.org/documentation/current/reference-manual/file-formats.html#mdp) and modify/extend it according to your needs. ---
**Author:** ![sajjadnej](https://avatars.discourse-cdn.com/v4/letter/s/e274bd/32.png) [@sajjadnej](https://ask.bioexcel.eu/u/sajjadnej)\ **Post date:** [October 31, 2023, 1:01pm UTC](https://ask.bioexcel.eu/t/problem-running-gromacs-simulation/4620/13 "2023-10-31T13:01:22Z")
Sorry for bothering you again. I have two problems. First, I don’t see any rmsf plot in the result analysis section. Does the analysis section provide us with rmsf plot? If not, how can I generate them? Second, I tried to do the md simulation for 100ns (100000ps) but after the completion of the project workflow the rmsd plot only showed 50ns. What is the problem? Thanks in advance. ---
**Author:** ![adam.hospital](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/adam.hospital/32/151_2.png) [@adam.hospital](https://ask.bioexcel.eu/u/adam.hospital)\ **Post date:** [October 31, 2023, 1:55pm UTC](https://ask.bioexcel.eu/t/problem-running-gromacs-simulation/4620/14 "2023-10-31T13:55:43Z")
Hi, RMSf can be computed with the “Protein MD Analysis” workflow, take a look here: [Help - BioExcel Building Blocks Workflows](https://mmb.irbbarcelona.org/biobb-wfs/help/workflows#mdprot_analysis) You can also use the [cpptraj\_rmsf](https://biobb-analysis.readthedocs.io/en/latest/ambertools.html#module-ambertools.cpptraj_rmsf) tool from the [biobb\_analysis](https://github.com/bioexcel/biobb_analysis) module. About the length of the simulation, it is difficult for me to figure out where the problem is, I would need more information, such as how did you run the production MD, with which program, with which input parameters, etc. I recommend you to carefully read the log files and try to understand why the simulation stopped at 50ns. ---
**Author:** ![sajjadnej](https://avatars.discourse-cdn.com/v4/letter/s/e274bd/32.png) [@sajjadnej](https://ask.bioexcel.eu/u/sajjadnej)\ **Post date:** [October 31, 2023, 8:30pm UTC](https://ask.bioexcel.eu/t/problem-running-gromacs-simulation/4620/15 "2023-10-31T20:30:32Z")
Thank you for your quick response. Unfortunately I deleted the project but I will try to rerun it and do as you said. ---
**Author:** ![sajjadnej](https://avatars.discourse-cdn.com/v4/letter/s/e274bd/32.png) [@sajjadnej](https://ask.bioexcel.eu/u/sajjadnej)\ **Post date:** [November 1, 2023, 6:25pm UTC](https://ask.bioexcel.eu/t/problem-running-gromacs-simulation/4620/16 "2023-11-01T18:25:54Z")
Hi, I tried to generate an RMSF plot from where you said. I used two files from the MD simulation result file that were generated by your server but after launching the project it stopped working. Would you please help me? I attached the screenshots of error and files that I used as trajectory and topology. Are these files correct? ![](https://europe1.discourse-cdn.com/flex013/uploads/bioexcel/original/1X/818cd1fcc139f91fdb0fb4b1957ace29d0961dd3.jpeg) ---
**Author:** ![adam.hospital](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/adam.hospital/32/151_2.png) [@adam.hospital](https://ask.bioexcel.eu/u/adam.hospital)\ **Post date:** [November 1, 2023, 8:53pm UTC](https://ask.bioexcel.eu/t/problem-running-gromacs-simulation/4620/17 "2023-11-01T20:53:33Z")
Hi, the protein analysis workflow is designed to work with a dehydrated trajectory. The files you selected are the correct ones, but you need to post-process them, removing counterions and water molecules before using them as input files for the Protein Analysis workflow. This is the result of doing this process: > **[Output summary for project Test sajjad Analysis - BioExcel Building Blocks...](https://mmb.irbbarcelona.org/biobb-wfs/trajectory/output/summary/6542b92b6eec74.49876977)** > > Workflow settings ---
**Author:** ![sajjadnej](https://avatars.discourse-cdn.com/v4/letter/s/e274bd/32.png) [@sajjadnej](https://ask.bioexcel.eu/u/sajjadnej)\ **Post date:** [November 2, 2023, 8:09am UTC](https://ask.bioexcel.eu/t/problem-running-gromacs-simulation/4620/19 "2023-11-02T08:09:57Z")
Thank you for your response. I didn’t quite get that. How can I remove ions and water for this process? ---
**Author:** ![adam.hospital](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/adam.hospital/32/151_2.png) [@adam.hospital](https://ask.bioexcel.eu/u/adam.hospital)\ **Post date:** [November 2, 2023, 9:20am UTC](https://ask.bioexcel.eu/t/problem-running-gromacs-simulation/4620/20 "2023-11-02T09:20:15Z")
Hi, there’s many different ways to do this. You can use any tool available for that (vmd, cpptraj, pytraj, mdanalysis, mdtraj, etc.) or use our BioExcel Building Blocks. You have an example of trajectory post-processing in the Protein-MD setup workflow here: [GROMACS Protein MD Setup tutorial - BioExcel Building Blocks](https://mmb.irbbarcelona.org/biobb/workflows/tutorials/md_setup#post) Hope it helps! ---
**Author:** ![sajjadnej](https://avatars.discourse-cdn.com/v4/letter/s/e274bd/32.png) [@sajjadnej](https://ask.bioexcel.eu/u/sajjadnej)\ **Post date:** [November 14, 2023, 8:53am UTC](https://ask.bioexcel.eu/t/problem-running-gromacs-simulation/4620/21 "2023-11-14T08:53:55Z")
Hi, I ran a gromacs md simulation job with a total time of 100ns but the results showed only 50ns. What is the problem? Would you please help me? I attached the workflow log. Thanks in advance. [workflow.pdf](https://ask.bioexcel.eu/uploads/short-url/y68ykDOZFkwbKOcPB1GXhEHGeRy.pdf) (139 KB) [Next page](https://ask.bioexcel.eu/t/problem-running-gromacs-simulation/4620.md?page=2)