# Downloading Energy Parameters, Hydrogen Bond Info, and SSE

**URL:** <https://ask.bioexcel.eu/t/downloading-energy-parameters-hydrogen-bond-info-and-sse/1715>\
**Category:** MDWeb\
**Created:** [October 10, 2019, 2:43am UTC](https://ask.bioexcel.eu/t/downloading-energy-parameters-hydrogen-bond-info-and-sse/1715 "2019-10-10T02:43:08Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![skhan21](https://avatars.discourse-cdn.com/v4/letter/s/e9a140/32.png) [@skhan21](https://ask.bioexcel.eu/u/skhan21)\
**Post date:** [October 10, 2019, 2:43am UTC](https://ask.bioexcel.eu/t/downloading-energy-parameters-hydrogen-bond-info-and-sse/1715/1 "2019-10-10T02:43:08Z")

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Hi,

I am looking for a way to download the energy parameters for MD simulations that I have run on MDWeb. Also, is it possible to download information on the number of intra-molecular hydrogen bonds or secondary structure elements (SSE)? If not, is there a way for me to get this data from GROMACS using a similar setup to MDWeb simulations?

Thanks

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**Author:** ![adam.hospital](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/adam.hospital/32/151_2.png) [@adam.hospital](https://ask.bioexcel.eu/u/adam.hospital)\
**Post date:** [October 10, 2019, 4:00pm UTC](https://ask.bioexcel.eu/t/downloading-energy-parameters-hydrogen-bond-info-and-sse/1715/2 "2019-10-10T16:00:45Z")

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Hi there,

first of all, check what you have run in MDWeb. If it is just a MD setup workflow, this will probably not give you enough information to extract dynamic properties of intra-molecular hydrogen bonds or secondary structure elements. You should probably run a longer simulation. That said, MDWeb does not have these analysis implemented unfortunately. GROMACS MD package on the other hand has a lot of analysis tools available to compute these properties. Check for example these commands:  
[http://manual.gromacs.org/documentation/2019/onlinehelp/gmx-do\_dssp.html](http://manual.gromacs.org/documentation/2019/onlinehelp/gmx-do_dssp.html)  
[http://manual.gromacs.org/documentation/2019/onlinehelp/gmx-hbond.html](http://manual.gromacs.org/documentation/2019/onlinehelp/gmx-hbond.html)

Hope it helps.

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