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] <javascript:>>
> 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
> >>> >
> >>> > --
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> >>>
> >>>
> >>> --
> >>> Christoph Junghans
> >>> Web: http://www.compphys.de
> >>>
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> >>
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>
>
> --
> Christoph Junghans
> Web: http://www.compphys.de
>
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