On Fri, Feb 2, 2018 at 5:09 AM, Adiran <d.smith.s...@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.

>
>
>>
>>
>> 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.
You could also try to fit the long-range tail of the PMF to get the
charges.
Are you planning on coarse graining the solvent away?

>
>>
>>
>> >
>> >
>> >
>> >>
>> >>
>> >> >
>> >> > 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"?

>
>>
>>
>> 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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>> >>
>> >>
>> >> --
>> >> 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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