[gmx-developers] Energy analysis

David van der Spoel spoel at xray.bmc.uu.se
Wed May 7 16:49:35 CEST 2014

On 2014-04-24 21:30, Berk Hess wrote:
> Hi,
> That is good news. The current code is far too complex to easily
> understand even the most basic functionality of g_energy.

Indeed. I got quite far already, just wondering if anyone is still using:
- the einstein relation for computing the viscosity
- the free energy estimate code

or whether I can drop those?

> Cheers,
> Berk
> On 04/24/2014 12:29 PM, David van der Spoel wrote:
>> Hi,
>> I would like to work on moving the energy analysis g_energy.c to C++
>> and to make the code somewhat reusable. For some trajectory analysis
>> tools this would be handy as well (for instance if you want to extract
>> the temperature). Before I embark on a lot of coding some quick
>> feedback would be appreciated. My plan is to
>> - create directory energyanalysis with code with a simple class
>> interface for extracting information from .edr (and later on .tng) files
>> - include energy based analyses (now in g_energy) in the class
>> - make an energy.cpp tool with the command line interface part, but
>> that calls the underlying class.
>> Comments?

David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se

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