[gmx-users] short peptide adsorption to a solid surface
josip7lovric at gmail.com
Mon Aug 1 13:35:43 CEST 2016
in gromacs you have lots of implemented tools for analysis like to compute
energy between surfacant and surface by energy groups, tilt angle, order
parameter, angle distribution,... But I would suggest you first to look in
previous publication connected with your studies, that could give you some
ideas and also give you better general understanding.
2016-08-01 12:48 GMT+02:00 Alexander Alexander <alexanderwien2k at gmail.com>:
> Dear gromacs user,
> I am study the adsorption of a short peptide into a solid surface, I have
> the outputs of a long MD simulation in which I see the peptide come to the
> surface and lie down on the surface, would you please suggest me some
> available tools in gromacs which I can take benefit in order to to study
> such an adsorption, for example to unveil the behavior and role of each
> residue in this adsorption, the C and N terminals ... .
> I have already used "gmx pairdist" to see the distance of each residue to
> the surface, what informative tools else you would do, please?
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