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Re: [ESPResSo] Espresso: Surface Force Analysis


From: duenweg
Subject: Re: [ESPResSo] Espresso: Surface Force Analysis
Date: Sat, 5 Jul 2008 15:32:42 +0200 (CEST)
User-agent: SquirrelMail/1.4.9a

Hello,

I don't quite understand the question.

As far as my understanding goes,
Molecular Dynamics runs via interaction
potentials, and forces derived from those
A stress tensor, on the contrary, is a
macroscopic quantity, derived from the
interactions and particle motions only
after averaging, typically via the virial
theorem. See any textbook like e.g.
Frenkel-Smit, Allen-Tildesley etc.

Or did I completely misunderstand your
problem?

Best regards
Burkhard Duenweg.



> Dear Espresso Community
>
> We are interested in intra-molecular forces in larger molecules, namely
> proteins. Ideally we would like to study surface forces on proteins, to
> then relate the forces to protein folding and inter-molecular
> interactions. We are not quite sure how to currently proceed with
> Espresso.
>
> One approach we have thought about is the stress tensor, but we are
> uncertain whether its algorithm and output will help us much.
>
> Is it true that a bonded stress tensor, such as the FENE stress tensor, is
> derived from the potential-distance curves between two particles, yielding
> the external force part in the stress tensor algorithm? In any case, would
> it be possible to use the stress tensor for this kind of analysis? A local
> stress tensor might be able to display forces, if we can define a volume
> element relative to an intra-molecular bond during a simulation, where we
> would have to update the xyz coordinates of the volume element for each
> time step.
>
> The stress tensor approach might not be the right approach if Espresso has
> a way to displaying outputs for the force fields, or forces exerted upon
> an atom. We are not sure about a command from the User Guide, but this
> could probably be done by looking deeper at the algorithms.
>
> I appreciate any help on this matter, and ideas for other approaches.
> Thank you.
>
> Sincerely,
>
> Vincent B├╝rger
>
> --
> Master of Advanced Materials and Processes
> Friedrich Alexander University Erlangen-Nuremberg
> address@hidden
>
>
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