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 
> <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,  <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?

 

>
> 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 
> >> >> <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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