# Atomistic simulation

**URL:** <https://gromacs.bioexcel.eu/t/atomistic-simulation/11835>\
**Category:** User discussions\
**Tags:** mdrun\
**Created:** [March 28, 2025, 9:36pm UTC](https://gromacs.bioexcel.eu/t/atomistic-simulation/11835 "2025-03-28T21:36:09Z")\
**Posts on this page:** 1\
**Page:** 1

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**Author:** ![js\_gro](https://avatars.discourse-cdn.com/v4/letter/j/ac8455/32.png) [@js\_gro](https://gromacs.bioexcel.eu/u/js_gro)\
**Post date:** [March 28, 2025, 9:36pm UTC](https://gromacs.bioexcel.eu/t/atomistic-simulation/11835/1 "2025-03-28T21:36:09Z")

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GROMACS version: 2018  
GROMACS modification: No

I am placing pure extended chains within their cutoff distance, but the box size is large with significant vacuum. Should I deform the box first and then perform NPT at high temperature? The system appears to be kinetically trapped—what are some possible ways to overcome this?