El jueves, 1 de febrero de 2018, 19:33:50 (UTC), sikandar escribió: > > Daniel, > > In regards to extending relative entropy implementation in VOTCA, it is > possible but not trivial. >
Yes it seems possible, as I understand it, in this paper it's done: https://pubs.acs.org/doi/abs/10.1021/jp2114994 > Hybrid approach of BI for bonded and Relative entropy for non-bonded can > work. So as a starting point, you can use BI for bonded interaction. For > extending relative entropy implementation to bonded interactions, see the > current implementation in csg source code at src/tools/csg_reupdate.cc . > Mainly you would need to implement function void > CsgREupdate::AAavgBonded(PotentialInfo* > potinfo) . There other things also you need to take care regarding > reading, writing bond interaction parameters, and generating bond > interaction tables for CG MD simulations. > > Thanks, > Sikandar > > > > On Thu, Feb 1, 2018 at 10:12 AM, Christoph Junghans <[email protected] > <javascript:>> wrote: > >> On Wed, Jan 31, 2018 at 11:14 AM, Adiran <[email protected] >> <javascript:>> 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? >> That is more a question for Sikandar! >> >> > >> >> >> >> >> >> > >> >> > 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? >> Transferability is very system-dependent, so you will have check that >> for your specific system. >> >> Also sec Section 2.2.1 of the manual <http://doc.votca.org/manual.pdf> >> > >> > 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. >> You can include the coulomb in the tabulated interactions so leave >> them separate if you know the CG charges. >> >> > >> > >> > >> >> >> >> >> >> > >> >> > 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: >> VOTCA will add the cutoff scheme automatically to the mdp file at >> iteration time if it isn't already in the mdp file. >> >> Did the tutorials without modification work? >> >> Christoph >> >> > >> >> > 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] <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.
