[gmx-users] free energy landscape question
baptista at itqb.unl.pt
baptista at itqb.unl.pt
Wed Jun 23 19:49:51 CEST 2010
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).
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
Have a nice landscaping,
> Any ideas?
> Many thanks,
> 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.
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Antonio M. Baptista
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