El viernes, 2 de febrero de 2018, 16:44:45 (UTC+1), Christoph Junghans escribió: > > On Fri, Feb 2, 2018 at 5:09 AM, Adiran <[email protected] <javascript:>> > wrote: > > > > > > 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]> 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? > Transferability is really hard to predict! A dimer might work better, > but maybe you even need a trimer. > > Great. The problem is that a trimer might be too big for AA...
> > > > > >> > >> > >> Also sec Section 2.2.1 of the manual <http://doc.votca.org/manual.pdf> > > > > > > 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? > Unfortunately, there is currently no optimization strategy in VOTCA. > What do you mean exactly by that? > You could also try to fit the long-range tail of the PMF to get the > charges. > How wouldl this work? > Are you planning on coarse graining the solvent away? > Yes. Do you have any suggestions? > > > > >> > >> > >> > > >> > > >> > > >> >> > >> >> > >> >> > > >> >> > 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. > What do you mean with "poor compilation"? > I mean very little optimized. For example, the GROMACS that I got via the script is not using MPI, GPUs nor MKL. I need to look into this and I will report back. Appart from having a proper GROMACS are there any other recommendations to optimize VOTCA itself? > > > > >> > >> > >> 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]. > >> > > >> > 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. 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