[gmx-users] free energy landscape question

[Andrei Neamtu]

Dear Antonio,
thank you.
I think I got the idea. I need to use a cut-off for the probability:
for all the probabilities lower than a certain value I assign to them
that (lower) value so the energy will be constant.

Thanks,
Andrei

On Wed, Jun 23, 2010 at 8:49 PM,  <baptista at itqb.unl.pt> wrote:
>
> On Wed, 23 Jun 2010, Andrei Neamtu wrote:
>
>> Dear Andreas and Marc,
>> Thanks for your reply.
>> I am not familiar with the gromacs programming code and so I am trying
>> to build myself the FEL.
>> I can generate the hisotgram of the number of states from the
>> projection along principal component 1 and 2 (PC1 and PC2) using
>> SigmaPlot but here I am stucked!
>>
>> I think that I have to compute the free energy with the formula G = -
>> kT ln(Pi/Pmax) where Pi is the probability of the state i (determined
>> py a certain pair of values of PC1 and PC2) and Pmax is the maximum
>> probability. But for certain there are regions in the principal
>> component plane with probabiliy zero which constitutes singularities
>> for the above formula (infinite energy).
>
> Hi Andrei,
>
> You can simply assign to those regions a very high energy value (e.g.,
> 100RT) that works as "+infinite". In practice, this doesn't matter, since
> you will always use an energy cutoff much lower than that when plotting or
> projecting your landscape.
>
>> From my experience, you should also pay attention to the choice of bin
>
> size and the eventual use of smoothing methods, especially if you are
> thinking about going to 3D or higher-dimensional histograms. We ended up
> using kernel density estimates instead of histograms
> (http://dx.doi.org/10.1021/jp902991u).
>
> Have a nice landscaping,
> Antonio
>
>>
>> Any ideas?
>>
>> Many thanks,
>> Andrei
>>
>> On Wed, Jun 23, 2010 at 12:34 PM, Marc F. Lensink
>> <lensink at bigre.ulb.ac.be> wrote:
>>>
>>> On Wed, Jun 23, 2010 at 10:20:19AM +0100, Kukol, Andreas wrote:
>>>>
>>>> Yes, that is an interesting question. I don't know the answer, but is
>>>> there any way to get the numerical values of the matrix from Gromacs tools
>>>> that produce a matrix in xpm format ? I have problems with g_rms and
>>>> g_rmsdist is another candidate.
>>>
>>> probably the easiest is to look at the code and print out the matrix
>>> before it's sent to the xpm plotting routine.
>>>
>>> you can also convert the xpm afterwards, but I guess the data then
>>> gets quantized.
>>>
>>> cheers,
>>> marc
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>
> --
> Antonio M. Baptista
> Instituto de Tecnologia Quimica e Biologica, Universidade Nova de Lisboa
> Av. da Republica - EAN
> 2780-157 Oeiras, Portugal
> phone: +351-214469619         email: baptista at itqb.unl.pt
> fax:   +351-214411277         WWW:   http://www.itqb.unl.pt/~baptista
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