[gmx-users] free energy landscape question

Andrei Neamtu neamtuandrei at gmail.com
Wed Jun 23 14:52:53 CEST 2010

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).

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.
> cheers,
> marc
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