Hi Daniel, Are you running the spce/re entropy tutorial? Please make sure GSL library is linked properly, sometimes there is an issue in linking to GSL due to which relative entropy update fails.
-- Sikandar On Wed, Jan 31, 2018 at 11:14 AM, Adiran <[email protected]> wrote: > > > El miércoles, 31 de enero de 2018, 15:30:03 (UTC), Christoph Junghans > escribió: >> >> 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! >> > > Great. Would it be very difficult? > > >> >> > >> > 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. >> > > > Right, so if the AA simulation contains just one protein plus solvent then > the parameters would be only optimized for intra-molecular interactions. > Would these also be transferable to a box with many proteins to simulate, > for example, aggregation? How does one deal with inter-molecular > interactions in the VOTCA scheme? > > I guess simulating a dimer AA would improve the results but that wouldn't > still be representative of the real situation. > > Also, with respect to the force field: > > As I understand it any form of potential (including coulomb) is acceptable > as long as you express it as an interpolation with splines. > > > > >> >> > >> > 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. >> > > I did that > > I have done that. Now I get a different error (when running the spce RE > tests) > > An error occurred: > Hessian NOT a positive definite! > This can be a result of poor initial guess or ill-suited CG potential > settings or poor CG sampling. > > I compiled using: > > ./build.sh --prefix ${prefix} --minimal -DWITH_GMX=ON -DWITH_FFTW=ON > -DWITH_GSL=ON -DGSL_INCLUDE_DIR=/usr/local/Cellar/gsl/2.4/include > -DGSL_LIBRARY=/usr/local/Cellar/gsl/2.4/lib/libgsl.dylib > -DCBLAS_LIBRARY=/usr/local/Cellar/gsl/2.4/lib/libgslcblas.dylib > -DFFTW3_INCLUDE_DIR=/usr/local/Cellar/fftw/3.3.7_1/include > -DFFTW3_LIBRARY=/usr/local/Cellar/fftw/3.3.7_1/lib/libfftw3.dylib gromacs > tools csg > > But then that gets translated into: > > cmake -DCMAKE_INSTALL_PREFIX='/Users/agaraizar/votca/' > --no-warn-unused-cli -DWITH_FFTW=OFF -DWITH_GSL=OFF > -DCMAKE_DISABLE_FIND_PACKAGE_GSL=ON -DWITH_MKL=OFF > -DCMAKE_DISABLE_FIND_PACKAGE_MKL=ON -DBUILD_MANPAGES=OFF -DWITH_GMX=OFF > -DWITH_SQLITE3=OFF -DWITH_H5MD=OFF -DCMAKE_DISABLE_FIND_PACKAGE_HDF5=ON > -DWITH_GMX=ON -DWITH_FFTW=ON -DWITH_GSL=ON > -DGSL_INCLUDE_DIR=/usr/local/Cellar/gsl/2.4/include > -DGSL_LIBRARY=/usr/local/Cellar/gsl/2.4/lib/libgsl.dylib > -DCBLAS_LIBRARY=/usr/local/Cellar/gsl/2.4/lib/libgslcblas.dylib > -DFFTW3_INCLUDE_DIR=/usr/local/Cellar/fftw/3.3.7_1/include > -DFFTW3_LIBRARY=/usr/local/Cellar/fftw/3.3.7_1/lib/libfftw3.dylib > -DCMAKE_INSTALL_RPATH_USE_LINK_PATH=ON /Users/agaraizar/votca/src/csg > > Thank you > > >> 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. > -- You received this message because you are subscribed to the Google Groups "votca" group. 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