# Average structure of the trajectory

**URL:** <https://gromacs.bioexcel.eu/t/average-structure-of-the-trajectory/308>\
**Category:** User discussions\
**Created:** [June 14, 2020, 5:10pm UTC](https://gromacs.bioexcel.eu/t/average-structure-of-the-trajectory/308 "2020-06-14T17:10:26Z")\
**Posts on this page:** 6\
**Page:** 1

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**Author:** ![Bhagya](https://avatars.discourse-cdn.com/v4/letter/b/c77e96/32.png) [@Bhagya](https://gromacs.bioexcel.eu/u/Bhagya)\
**Post date:** [June 14, 2020, 5:10pm UTC](https://gromacs.bioexcel.eu/t/average-structure-of-the-trajectory/308/1 "2020-06-14T17:10:27Z")

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GROMACS version:  
GROMACS modification: No

Hi,

I need to get an average structure from the multimolecular ( 125 of same short-chain molecules) trajectory? The average structure should be a single molecule. Can someone pls help me on this ?

Regards  
Bhagya

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**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\
**Post date:** [June 15, 2020, 1:44am UTC](https://gromacs.bioexcel.eu/t/average-structure-of-the-trajectory/308/2 "2020-06-15T01:44:41Z")

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Why do you need an average structure of 125 molecules? It will be unphysical.

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<div class="post-metadata">

**Author:** ![Bhagya](https://avatars.discourse-cdn.com/v4/letter/b/c77e96/32.png) [@Bhagya](https://gromacs.bioexcel.eu/u/Bhagya)\
**Post date:** [June 15, 2020, 2:06am UTC](https://gromacs.bioexcel.eu/t/average-structure-of-the-trajectory/308/3 "2020-06-15T02:06:56Z")

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we want it for representation purposes. Please help me.

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**Author:** ![Er1ck](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/er1ck/32/132_2.png) [@Er1ck](https://gromacs.bioexcel.eu/u/Er1ck)\
**Post date:** [June 15, 2020, 2:29am UTC](https://gromacs.bioexcel.eu/t/average-structure-of-the-trajectory/308/4 "2020-06-15T02:29:31Z")

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Maybe just pick one frame that looks representable.

I wonder if you are looking for the molecular geometry at energy minimization.  
If that is the case, you just need the output from the energy minimization.

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<div class="post-metadata">

**Author:** ![Bhagya](https://avatars.discourse-cdn.com/v4/letter/b/c77e96/32.png) [@Bhagya](https://gromacs.bioexcel.eu/u/Bhagya)\
**Post date:** [June 15, 2020, 3:53am UTC](https://gromacs.bioexcel.eu/t/average-structure-of-the-trajectory/308/5 "2020-06-15T03:53:41Z")

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In my system I have 125 identical molecules. I want to see the average structure of that. Need to get an idea about how it’s in bulk system. Please help me

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**Author:** ![Er1ck](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/er1ck/32/132_2.png) [@Er1ck](https://gromacs.bioexcel.eu/u/Er1ck)\
**Post date:** [June 15, 2020, 5:04pm UTC](https://gromacs.bioexcel.eu/t/average-structure-of-the-trajectory/308/6 "2020-06-15T17:04:37Z")

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If your system reach equilibrium, there shouldn’t be any difference in bulk property and final output would be representable.