On Wed, Jan 31, 2018 at 3:50 AM, <[email protected]> wrote: > El miércoles, 31 de enero de 2018, 5:26:35 (UTC), sikandar escribió: >> >> 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. > > > Is there a plan to include them soon? Not really, but patches are always welcome!
> > So, if I understood correctly, one would create a suitable CG force field > and then would minimize the non-bonded parameters with RE and the bonded > ones with Boltzmann inversion in a semi-decoupled way? Yes, do BI first and then use the bonded table in the CG run with RE as fixed interactions. > > Also, I am having trouble running the RE tutorials, for example in the > methanol and water one: firstly it doesn't run without me manually changing > the .mdp file to specify the cutoff scheme to be group and then it is > terminated with: > > begin to calculate distribution functions > # of bonded interactions: 0 > # of non-bonded interactions: 3 an error occurred: > input format not supported: topol.tpr This error means you have compiled VOTCA without gromacs. Just re-run cmake with -DWITH_GMX=ON and rebuild with "make" again. Christoph > > The GROMACS version I am using is the one provided by VOTCA in the build > script > > GROMACS: gmx, version 2016.5-dev-20180109-aa8b47218-unknown Executable: > /Users/agaraizar/votca/bin/gmx > > In the mailing list someone had a similar issue but in her case she hadn't > installed GROMACS > > Regards, > > Adiran > >> >> 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 > > > Thank you > >> >> >> >> --- >> 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. >>> > > Thank you for your answer Christoph > >>> >>> 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. -- 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.
