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, <bapti...@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 >> <lens...@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 >>> -- >>> gmx-users mailing list gmx-us...@gromacs.org >>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>> Please search the archive at http://www.gromacs.org/search before >>> posting! >>> Please don't post (un)subscribe requests to the list. Use the >>> www interface or send it to gmx-users-requ...@gromacs.org. >>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >>> >> -- >> gmx-users mailing list gmx-us...@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search before posting! >> Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > > -- > 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: bapti...@itqb.unl.pt > fax: +351-214411277 WWW: http://www.itqb.unl.pt/~baptista > -------------------------------------------------------------------------- > -- > gmx-users mailing list gmx-us...@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php