Daniel, I cannot talk to efficiency of the relative entropy method, but in general coarse-graining a protein is hard. You need to have a good intuition how to do the mapping and which interaction to consider.
VOTCA has support for running RDF, IMC and relative entropy calculation in parallel. In addition you can speed up the gromacs runs by using a parallel gromacs as well. Christoph On Tue, Jan 30, 2018 at 5:17 AM, <[email protected]> wrote: > Dear all, > > After reading a lot of the literature available on relative entropy > minimization as a coarse graining technique I am extremely keen on using it > for my research. > > I was wondering wether it would be possible/feasible (in a reasonable amount > of time) to use VOTCA to coarse grain a protein (~500 atoms) using RE. > > I am also not sure about what if any parallelization VOTCA has that would > reduce the required time (and if it does how to use it). > > Would having a parallel GROMACS help? > > Regards and thanks in advance, > > Daniel > > -- > You received this message because you are subscribed to the Google Groups > "votca" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to [email protected]. > To post to this group, send email to [email protected]. > Visit this group at https://groups.google.com/group/votca. > For more options, visit https://groups.google.com/d/optout. -- Christoph Junghans Web: http://www.compphys.de -- You received this message because you are subscribed to the Google Groups "votca" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To post to this group, send email to [email protected]. Visit this group at https://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
