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 <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 <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?
 

> 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 
> >> >> >> <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 
> >> >> >>> > 
> >> >> >>> > -- 
> >> >> >>> > 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 votca+un...@googlegroups.com. 
> >> >> >>> > To post to this group, send email to vo...@googlegroups.com. 
> >> >> >>> > 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 votca+un...@googlegroups.com. 
> >> >> >>> To post to this group, send email to vo...@googlegroups.com. 
> >> >> >>> 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 votca+un...@googlegroups.com. 
> >> >> > To post to this group, send email to vo...@googlegroups.com. 
> >> >> > 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 votca+un...@googlegroups.com. 
> >> > 
> >> > To post to this group, send email to vo...@googlegroups.com. 
> >> > 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 votca+un...@googlegroups.com <javascript:>. 
> > To post to this group, send email to vo...@googlegroups.com 
> <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.
To unsubscribe from this group and stop receiving emails from it, send an email 
to votca+unsubscr...@googlegroups.com.
To post to this group, send email to votca@googlegroups.com.
Visit this group at https://groups.google.com/group/votca.
For more options, visit https://groups.google.com/d/optout.

Reply via email to