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? 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? 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 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] > <javascript:>> 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] <javascript:>> >> 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] <javascript:>. >> > To post to this group, send email to [email protected] >> <javascript:>. >> > 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] <javascript:>. >> To post to this group, send email to [email protected] <javascript:> >> . >> 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.
