Hi Daniel, It is possible to use relative entropy implementation in VOTCA to coarse-grain protein. At this point, relative entropy implementation in VOTCA supports only non-bonded interaction coarse-graining. For bonded interaction you will need to use Boltzmann inversion or other suitable method. VOTCA does support multithreaded parallel processing of MD trajectories and parallel MD simulations using GROMACS. For details about the relative entropy implementation and parallel performance of VOTCA you can refer to the PLOS One article https://doi.org/10.1371/journal.pone.0131754
--- Sikandar On Tue, Jan 30, 2018 at 10:26 AM, Christoph Junghans <[email protected]> wrote: > 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. > -- 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.
