# Different masses of dummy atoms in webserver pmx and standalone pmx

**URL:** <https://ask.bioexcel.eu/t/different-masses-of-dummy-atoms-in-webserver-pmx-and-standalone-pmx/4612>\
**Category:** pmx\
**Created:** [October 18, 2023, 2:06pm UTC](https://ask.bioexcel.eu/t/different-masses-of-dummy-atoms-in-webserver-pmx-and-standalone-pmx/4612 "2023-10-18T14:06:56Z")\
**Posts on this page:** 1\
**Showing post:** 2

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**Author:** ![Sudchem](https://avatars.discourse-cdn.com/v4/letter/s/ecccb3/32.png) [@Sudchem](https://ask.bioexcel.eu/u/Sudchem)\
**Post date:** [October 31, 2023, 9:08am UTC](https://ask.bioexcel.eu/t/different-masses-of-dummy-atoms-in-webserver-pmx-and-standalone-pmx/4612/2 "2023-10-31T09:08:27Z")

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Hi Mary,

The recent version of pmx (develop branch) applies a scaling factor of 0.33 by default. Hence, the DUM\_C has a mass of 12.01\*0.33=3.9633. The web server uses an old version of pmx, in which the mass of a dummy is 1.0 by default. The scaling factor is used to maintain the stability of a simulated system.  
You can read this thread for more on the discussion: [Oscillational period warning during tripeptide A2I forward simulation](https://ask.bioexcel.eu/t/oscillational-period-warning-during-tripeptide-a2i-forward-simulation/4034)

Using either of the itp files should be fine provided that your simulation is stable (no oscillation-period-warning). The mass of the dummy particle will not have much effect on the ddG prediction.

Best,  
Sudarshan

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