# Performing coarse grained simulation on protein alone **URL:** \ **Category:** User discussions\ **Created:** [January 26, 2021, 11:10pm UTC](https://gromacs.bioexcel.eu/t/performing-coarse-grained-simulation-on-protein-alone/1491 "2021-01-26T23:10:45Z")\ **Posts on this page:** 9\ **Page:** 1
**Author:** ![dkd54](https://avatars.discourse-cdn.com/v4/letter/d/c4cdca/32.png) [@dkd54](https://gromacs.bioexcel.eu/u/dkd54)\ **Post date:** [January 26, 2021, 11:10pm UTC](https://gromacs.bioexcel.eu/t/performing-coarse-grained-simulation-on-protein-alone/1491/1 "2021-01-26T23:10:45Z")
GROMACS version: 2018.3 GROMACS modification: Yes/No Hi gmx users, To introduce myself, I perform all-atom AMBER MD on proteins. This is my first attempt into the gromacs and coarse graining domain. I wish to perform coarse graining simulation on individual protein systems (without any ligand). My objective is to CG simulate the protein long enough to check if there are any major conformational changes happening over an extended period of time (2-3 microseconds). I have been reading a lot about coarse graining but I’m confused because I didn’t find relevant information on performing coarse graining on individual monomeric proteins. I have successfully installed the above mentioned version of gromacs though. Please let me know if this can be done. If yes then where should I start or find a decent tutorial/protocol for doing that. Thank you all in advance. ---
**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\ **Post date:** [January 27, 2021, 1:59pm UTC](https://gromacs.bioexcel.eu/t/performing-coarse-grained-simulation-on-protein-alone/1491/2 "2021-01-27T13:59:40Z")
[http://cgmartini.nl/index.php/tutorials-general-introduction-gmx5/proteins-gmx5](http://cgmartini.nl/index.php/tutorials-general-introduction-gmx5/proteins-gmx5) ---
**Author:** ![dkd54](https://avatars.discourse-cdn.com/v4/letter/d/c4cdca/32.png) [@dkd54](https://gromacs.bioexcel.eu/u/dkd54)\ **Post date:** [January 28, 2021, 9:26pm UTC](https://gromacs.bioexcel.eu/t/performing-coarse-grained-simulation-on-protein-alone/1491/3 "2021-01-28T21:26:09Z")
Hi @jalemkul and others, Thanks, the tutorial was very helpful. I was able to successfully carry out each step till the production run using the sample files. I have one question though. As I stated earlier, I wish to perform an extended production run of 2 microseconds. Usually in all atom MD simulation, I tweak the ‘nstlim’ in the production-input file to achieve that. I tried to do the same here in the dynamic.mdp file. I changed the nsteps to 70000000 (and dt=0.03ps), which would give me a simulation time of 2.1 microsecond. However, when I execute the production run using the ‘gmx mdrun -deffnm dynamic -v’ command, it still runs only for the default 3000000 steps. What am I doing wrong here? Thanks for your help in advance. ---
**Author:** ![kevinboyd](https://avatars.discourse-cdn.com/v4/letter/k/c77e96/32.png) [@kevinboyd](https://gromacs.bioexcel.eu/u/kevinboyd)\ **Post date:** [January 31, 2021, 6:51pm UTC](https://gromacs.bioexcel.eu/t/performing-coarse-grained-simulation-on-protein-alone/1491/4 "2021-01-31T18:51:34Z")
Did you re-generate the TPR? Changing the mdp options won’t do anything if you use the old tpr file. ---
**Author:** ![dkd54](https://avatars.discourse-cdn.com/v4/letter/d/c4cdca/32.png) [@dkd54](https://gromacs.bioexcel.eu/u/dkd54)\ **Post date:** [February 1, 2021, 4:38pm UTC](https://gromacs.bioexcel.eu/t/performing-coarse-grained-simulation-on-protein-alone/1491/5 "2021-02-01T16:38:08Z")
Hi @kevinboyd Yes, I did. First I ran this command to regenerate the new tpr: `gmx convert-tpr -s dynamic.tpr -extend 67000000 -o dynamic_extended.tpr` This command ran without any issues. Then, I ran this command: `gmx mdrun -s dynamic_extended.tpr -cpi dynamic_prev.cpt` But, it gave me the following error: Command line: gmx mdrun -s dynamic\_extended.tpr -cpi dynamic\_prev.cpt Output file appending has been requested, but some output files listed in the checkpoint file dynamic\_prev.cpt are not present or not named as the output files by the current program: Expect output files present: Expected output files not present or named differently: dynamic.log dynamic.xtc dynamic.edr Program: gmx mdrun, version 2018.2 Source file: src/gromacs/mdrunutility/handlerestart.cpp (line 179) Fatal error: File appending requested, but 3 of the 3 output files are not present or are named differently. For safety reasons, GROMACS-2016 and later only allows file appending to be used when all files have the same names as they had in the original run. Checkpointing is merely intended for plain continuation of runs. For safety reasons you must specify all file names (e.g. with -deffnm), and all these files must match the names used in the run prior to checkpointing since we will append to them by default. If you used -deffnm and the files listed above as not present are in fact present, try explicitly specifying them in respective mdrun options. If the files are not available, you can add the -noappend flag to mdrun and write separate new parts. For mere concatenation of files, you should use the gmx trjcat tool instead. For more information and tips for troubleshooting, please check the GROMACS website at [Errors - Gromacs](http://www.gromacs.org/Documentation/Errors) ---
**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\ **Post date:** [February 1, 2021, 5:00pm UTC](https://gromacs.bioexcel.eu/t/performing-coarse-grained-simulation-on-protein-alone/1491/6 "2021-02-01T17:00:31Z")
In the event that `mdrun` cannot append to files, it gives a fatal error, as shown, so you did not run the original number of steps again, you simply didn’t perform a new simulation. You can disable appending with `mdrun -noappend` to overcome the problem. ---
**Author:** ![dkd54](https://avatars.discourse-cdn.com/v4/letter/d/c4cdca/32.png) [@dkd54](https://gromacs.bioexcel.eu/u/dkd54)\ **Post date:** [February 1, 2021, 5:24pm UTC](https://gromacs.bioexcel.eu/t/performing-coarse-grained-simulation-on-protein-alone/1491/7 "2021-02-01T17:24:58Z")
Hi @jalemkul, Thank you so much. The -noappend flag fixed the fatal termination. Now, the simulation is running. Thanks again. ---
**Author:** ![dkd54](https://avatars.discourse-cdn.com/v4/letter/d/c4cdca/32.png) [@dkd54](https://gromacs.bioexcel.eu/u/dkd54)\ **Post date:** [February 17, 2021, 6:34pm UTC](https://gromacs.bioexcel.eu/t/performing-coarse-grained-simulation-on-protein-alone/1491/8 "2021-02-17T18:34:41Z")
@jalemkul The simulation ran and completed successfully. Further, I aim to visualize the RMSD and RMSF of the protein. Which commands do I use to analyze the trajectory? ---
**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\ **Post date:** [February 17, 2021, 6:51pm UTC](https://gromacs.bioexcel.eu/t/performing-coarse-grained-simulation-on-protein-alone/1491/9 "2021-02-17T18:51:07Z")
[https://manual.gromacs.org/current/user-guide/cmdline.html#distances-between-structures](https://manual.gromacs.org/current/user-guide/cmdline.html#distances-between-structures)