# Challenges in Reproducing ddG Estimation Results for 1STN

**URL:** <https://ask.bioexcel.eu/t/challenges-in-reproducing-ddg-estimation-results-for-1stn/4767>\
**Category:** pmx\
**Created:** [January 15, 2024, 7:07am UTC](https://ask.bioexcel.eu/t/challenges-in-reproducing-ddg-estimation-results-for-1stn/4767 "2024-01-15T07:07:21Z")\
**Posts on this page:** 1\
**Showing post:** 11

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**Author:** ![mstieffe](https://avatars.discourse-cdn.com/v4/letter/m/a698b9/32.png) [@mstieffe](https://ask.bioexcel.eu/u/mstieffe)\
**Post date:** [February 20, 2024, 10:17am UTC](https://ask.bioexcel.eu/t/challenges-in-reproducing-ddg-estimation-results-for-1stn/4767/11 "2024-02-20T10:17:43Z")

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Thank you very much for providing the mdp files. However, I have some questions regarding the velocity equilibration before the transition. In my current setup, I perform 20 ns equilibration runs for both the WT and MUT states. I then extract 100 equidistant frames from each of these runs and carry out a 50 ps transition for WT-\>MUT and MUT-\>WT, respectively. Is it necessary to perform velocity equilibration before the transitions in this setup?

I used your mdp files (for equilibration and transition) with GROMACS 2023.5 and the master branch of PMX, deploying the amber99sb-star-ildn-mut forcefield. I completed four runs each for F2A and I2A, obtaining -37.05±0.24 kJ/mol and -12.51±0.26 kJ/mol, respectively. The webserver reports -31.95±0.39 kJ/mol and -9.64±0.33 kJ/mol. Although the deviations are not overly large, they are still significant and do not appear to be outliers, as I consistently obtained these values over multiple separate runs. Interestingly, for the other two tripeptides I tested (V2A and L2A), I was able to perfectly reproduce the results from the webserver.

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