Downloading Energy Parameters, Hydrogen Bond Info, and SSE

MDWeb
1

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

2

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-hbond.html

Hope it helps.

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