El jueves, 1 de febrero de 2018, 18:12:34 (UTC), Christoph Junghans escribió: > > 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. >
I am not sure if I understand correctly. My intention is to create a CG model of a protein. Then use this model to be able to represent many proteins and study multimerization. My worry is: if I can only run an AA simulation of monomer then the inter-molecular interactions will not be really optimized no? If I use a dimer as the AA reference it might be better right? > > Also sec Section 2.2.1 of the manual <http://doc.votca.org/manual.pdf > <http://www.google.com/url?q=http%3A%2F%2Fdoc.votca.org%2Fmanual.pdf&sa=D&sntz=1&usg=AFQjCNHcKviJbOqIm-v-2sBvXrrnHdeM1w>> > > > That is helpful thank you. > > > > 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. > I can model them by solving a Poisson-Boltzmann equation but couldn't I get better guesses (or optimize the ones I have) from VOTCA? > > > > > > > > >> > >> > >> > > >> > 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? > In the end I managed to run them, yes, but with a very poor compilation. I will try a more aggressive one and report back any problems. > > 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]. 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.
