On Fri, Feb 2, 2018 at 11:43 AM, Adiran <d.smith.s...@gmail.com> wrote:
>
>
> 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 <d.smit...@gmail.com> 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 <d.smit...@gmail.com> wrote:
>> >> >
>> >> >
>> >> > El miércoles, 31 de enero de 2018, 15:30:03 (UTC), Christoph Junghans
>> >> > escribió:
>> >> >>
>> >> >> On Wed, Jan 31, 2018 at 3:50 AM, <d.smit...@gmail.com> 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?
I meant there is no charge optimization implemented in VOTCA!
>
>>
>> You could also try to fit the long-range tail of the PMF to get the
>> charges.
>
>
> How wouldl this work?
Alexander Lyubartsev (IMC) did that in one of this papers! Basically
you can derive the effective charges by fitting the tail of the
interaction.
>
>
>>
>> Are you planning on coarse graining the solvent away?
>
>
> Yes. Do you have any suggestions?
No really, doing implicit solvent saves you some computer power and
determination of CG parameters, but might hurt the chemical accuracy
of the simulation.
>
>>
>>
>> >
>> >>
>> >>
>> >> >
>> >> >
>> >> >
>> >> >>
>> >> >>
>> >> >> >
>> >> >> > 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?
Not really, for RE you need to compile VOTCA with gsl, so there aren't
many options for optimization.
And thread parallelization is enabled by default anyhow.
>
>>
>>
>> >
>> >>
>> >>
>> >> 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
>> >> >> >> <jung...@votca.org>
>> >> >> >> 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, <d.smit...@gmail.com> 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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>> >>
>> >>
>> >>
>> >> --
>> >> Christoph Junghans
>> >> Web: http://www.compphys.de
>> >
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>>
>>
>> --
>> Christoph Junghans
>> Web: http://www.compphys.de
>
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