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[ESPResSo] Espresso: Surface Force Analysis

From: Vincent . Buerger
Subject: [ESPResSo] Espresso: Surface Force Analysis
Date: Fri, 4 Jul 2008 12:28:00 +0200 (MEST)
User-agent: SquirrelMail/1.4.13

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

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.


Vincent B├╝rger

Master of Advanced Materials and Processes
Friedrich Alexander University Erlangen-Nuremberg

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