# \#user-guide

**URL:** https://gromacs.bioexcel.eu/tag/user-guide/14.md

[Latest](https://gromacs.bioexcel.eu/latest.md) · [Categories](https://gromacs.bioexcel.eu/categories.md) · [Tags](https://gromacs.bioexcel.eu/tags.md)

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## [I do not have the exact tpr file for a mdrun xtc, how to analyze](https://gromacs.bioexcel.eu/t/i-do-not-have-the-exact-tpr-file-for-a-mdrun-xtc-how-to-analyze/2720)

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**Author:** [@struc\_bio](https://gromacs.bioexcel.eu/u/struc_bio)\
**Replies:** 2\
**Last updated:** [August 25, 2021, 10:31pm UTC](https://gromacs.bioexcel.eu/t/i-do-not-have-the-exact-tpr-file-for-a-mdrun-xtc-how-to-analyze/2720 "2021-08-25T22:31:18Z")

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I have an xtc file from a md-run (performed last year) However, due to data loss, I have lost the relevant tpr file. How can I extract information about the simulation parameters, distance restrains, harmonic restraint…

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## [An error (possible bug) in the equation for updating velocity for stochastic dynamics](https://gromacs.bioexcel.eu/t/an-error-possible-bug-in-the-equation-for-updating-velocity-for-stochastic-dynamics/2585)

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**Author:** [@xzeng](https://gromacs.bioexcel.eu/u/xzeng)\
**Replies:** 0\
**Last updated:** [July 23, 2021, 5:29pm UTC](https://gromacs.bioexcel.eu/t/an-error-possible-bug-in-the-equation-for-updating-velocity-for-stochastic-dynamics/2585 "2021-07-23T17:29:20Z")

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GROMACS version: 2021.2 GROMACS modification: No Hi, the equation for updating velocity in stochastic dynamics, eq. 3.116 in reference manual 5.1 is not correct. 1-alpha^2 should be alpha\*(2-alpha), see the original re…

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## [Adding non-standard amino acid topologies to CHARMM36 using CHARMM-GUI](https://gromacs.bioexcel.eu/t/adding-non-standard-amino-acid-topologies-to-charmm36-using-charmm-gui/2270)

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**Author:** [@areyesromero](https://gromacs.bioexcel.eu/u/areyesromero)\
**Replies:** 1\
**Last updated:** [June 4, 2021, 5:27pm UTC](https://gromacs.bioexcel.eu/t/adding-non-standard-amino-acid-topologies-to-charmm36-using-charmm-gui/2270 "2021-06-04T17:27:11Z")

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GROMACS version: 2021 GROMACS modification: Yes/No Dear all, I have the include topology of my non-natural amino acid “aa-lig.itp” generated with Ligand Reader & Modeler. My goal is to add them to the CHARMM36 forcefi…