# \-noappend constant-pH MD **URL:** \ **Category:** User discussions\ **Created:** [June 3, 2025, 1:32pm UTC](https://gromacs.bioexcel.eu/t/noappend-constant-ph-md/12191 "2025-06-03T13:32:10Z")\ **Posts on this page:** 8\ **Page:** 1
**Author:** ![Marius](https://avatars.discourse-cdn.com/v4/letter/m/ed655f/32.png) [@Marius](https://gromacs.bioexcel.eu/u/Marius)\ **Post date:** [June 3, 2025, 1:32pm UTC](https://gromacs.bioexcel.eu/t/noappend-constant-ph-md/12191/1 "2025-06-03T13:32:10Z")
GROMACS version: 2021 GROMACS modification: constant-pH (Aho et al.) **Disclaimer:** The question was also posted [here](https://gitlab.com/gromacs-constantph/phbuilder/-/issues/37). Dear Users, we recently setup some constant-pH simulation (small molecule with multi-site representation) using the recent implementation by Aho et al. ([cpHMD](https://gitlab.com/gromacs-constantph)). For one of our setups, we used `gmx mdrun -noappend` to run the simulations on our local cluster. I then stumbled across the following warning in the manual: > `cphmd` command currently does not work with `.edr` files saved as separate part after continuation (when `-noappend` is used in `mdrun` ). We currently recommend all the users to append data to the initial files when continuing simulations. I am wondering now how this affects our simulations? Can we still use the data stored in the `.xtc` and `.edr` files, or should we repeat the simulations? The lambda-coordinates extracted from `md.part0001.edr` and `md.part0002.edr` appear to be correct. For example, `md.part0002.edr` starts at 11.006 ns, and its lambda-coordinates match exactly with those stored in `md.part0001.edr` at that time point. However, we encounter the following error for some simulations after the **second** append (e.g., for `md.part0003.edr`) using `gmx cphmd` or `gmx energy`: > Fatal error: > Energy header magic number mismatch, this is not a GROMACS edr file > If you want to use the correct frames before the corrupted frame and avoid > this fatal error set the env.var. GMX\_ENX\_NO\_FATAL I would greatly appreciate it if someone could provide a more detailed explanation of why the `-noappend` option should be avoided in constant-pH MD simulations, and whether the fatal error regarding a magic number mismatch is related to this. Thank you very much already in advance! All the best, Marius ---
**Author:** ![hess](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/hess/32/416_2.png) [@hess](https://gromacs.bioexcel.eu/u/hess)\ **Post date:** [June 4, 2025, 7:25am UTC](https://gromacs.bioexcel.eu/t/noappend-constant-ph-md/12191/2 "2025-06-04T07:25:50Z")
Which git commit are you using? I cannot find this cphmd error message in the code. ---
**Author:** ![Marius](https://avatars.discourse-cdn.com/v4/letter/m/ed655f/32.png) [@Marius](https://gromacs.bioexcel.eu/u/Marius)\ **Post date:** [June 4, 2025, 8:50am UTC](https://gromacs.bioexcel.eu/t/noappend-constant-ph-md/12191/3 "2025-06-04T08:50:27Z")
Hi @hess, if I do `git log` the latest entry in the downloaded repository (I did not run `git pull` since the installation) is: ```auto commit 28807b1162cacd9dc797520bc509d12edca13d1a (HEAD -> main, origin/main, origin/HEAD) Author: Berk Hess Date: Wed Apr 9 15:39:53 2025 +0200 Two fixes to enable compilation with gcc-13 ``` ---
**Author:** ![hess](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/hess/32/416_2.png) [@hess](https://gromacs.bioexcel.eu/u/hess)\ **Post date:** [June 4, 2025, 9:12am UTC](https://gromacs.bioexcel.eu/t/noappend-constant-ph-md/12191/4 "2025-06-04T09:12:22Z")
Ah, I see now that you pasted text from the manual, not an error message. Then this is unfortunately a limitation of the code. I don’t understand exactly what the issue is. Have you tried concatenating the files with eneconv? I guess that won’t work either. ---
**Author:** ![Marius](https://avatars.discourse-cdn.com/v4/letter/m/ed655f/32.png) [@Marius](https://gromacs.bioexcel.eu/u/Marius)\ **Post date:** [June 4, 2025, 10:27am UTC](https://gromacs.bioexcel.eu/t/noappend-constant-ph-md/12191/5 "2025-06-04T10:27:23Z")
The first block quote was pasted from the manual, and the last block quote is an actual error message raised by GROMACS. My question has two parts: 1. Does using `-noappend` affect the physical correctness of our simulations or any further analysis? From my understanding of the manual, the only drawback is that you must run `gmx cphmd` on each `.edr` file individually. This may make the analysis slightly more tedious, but the outputs should remain physically valid. 2. Could the corruption of the `.edr` files be caused by using `-noappend` in our cpHMD simulations, or is it more likely due to an issue with our file system? ---
**Author:** ![hess](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/hess/32/416_2.png) [@hess](https://gromacs.bioexcel.eu/u/hess)\ **Post date:** [June 5, 2025, 11:00am UTC](https://gromacs.bioexcel.eu/t/noappend-constant-ph-md/12191/6 "2025-06-05T11:00:02Z")
Yes, but it’s not clear to me if those two issues are separate. The results will be correct with -noappend. But it could be that using -noappend generates an unreadable edr file. ---
**Author:** ![Marius](https://avatars.discourse-cdn.com/v4/letter/m/ed655f/32.png) [@Marius](https://gromacs.bioexcel.eu/u/Marius)\ **Post date:** [June 5, 2025, 11:15am UTC](https://gromacs.bioexcel.eu/t/noappend-constant-ph-md/12191/7 "2025-06-05T11:15:40Z")
Okay that could explain our observation. Interestingly, it seems that not all our systems are affected by this issue. If I find some time I will try to investigate that issue a little bit more closely. For now, we will repeat the affected simulations with `-append`. Thank you very much! :) ---
**Author:** ![hess](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/hess/32/416_2.png) [@hess](https://gromacs.bioexcel.eu/u/hess)\ **Post date:** [June 5, 2025, 11:29am UTC](https://gromacs.bioexcel.eu/t/noappend-constant-ph-md/12191/8 "2025-06-05T11:29:24Z")
Maybe it’s related to the strange time of your checkpointing and it will work if checkpointing occurs at and nstenergy step.