[gmx-users] short peptide adsorption to a solid surface

Josip Lovrić josip7lovric at gmail.com
Mon Aug 1 13:35:43 CEST 2016

Dear Alexander,

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?
> Thanks,
> Regards,
> Aelx
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