[gmx-developers] Energy analysis

David van der Spoel spoel at xray.bmc.uu.se
Tue May 27 11:22:59 CEST 2014

On 2014-05-07 16:54, Berk Hess wrote:
> On 05/07/2014 04:47 PM, David van der Spoel wrote:
>> 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
> yes

I wonder how to interpret the results (more a user question but since 
I'm editing the code and don't understand the results I might as well 
clarify it).

So I get the Shear Viscosity Integral from the Einstein Viscosity code 
and this quickly converges to a constant value for my liquids. The unit 
given on the Y-axis is kg m^-1 s^-1 ps (which makes sense for a 
viscosity integral). However, if the unit is correct, the viscosity 
should be the slope of this curve, which is zero (since my curve is 
fluctuating around a constant value). Am I misunderstanding something?

>> - the free energy estimate code
> yes
>> or whether I can drop those?
> So I would vote for not dropping them.
> Berk
>>> 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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