Re: [votca] Coarse-graining of water in confinement

[Sikandar Mashayak]

Hi Christina,

We were able to reproduce water density distribution in slit-like pore
using relative entropy minimization method implemented in VOTCA. See the
details in reference https://aip.scitation.org/doi/abs/10.1063/1.4769297

Regards,
Sikandar

On Mon, May 20, 2019 at 6:19 AM CHRISTINA-ANNA GATSIOU <
christianna.gats...@gmail.com> wrote:

> Thanks Christoph! That was very helpful!
>
> > On 20 May 2019, at 4:09 PM, Christoph Junghans 
> wrote:
> >
> > On Mon, May 20, 2019 at 4:00 AM CHRISTINA-ANNA GATSIOU
> >  wrote:
> >>
> >> Hi,
> >>
> >> I have been trying to produce a CG force-field for a clay-water system
> (water confined in  a clay slit pore). Methods such as IBI does not really
> work for such systems. FM gave very poor results as well. I was wondering
> if VOTCA allows the use of alternative kind of distributions (instead of
> RDF, maybe Axial distributions) to perform IBI. Otherwise I would also be
> interested in any other methods that might work for such systems.
> >
> > There is slab IBI (https://github.com/votca/csg/issues/198), but it
> > never got merged.
> >
> > Otherwise you can use a different distribution, you just have to
> > overwrite the script, which calculates with RDF (calc_rdf_generic.sh)
> > with something else.
> >
> > In short, overwriting scripts works like this:
> > - make a new folder
> > - copy calc_rdf_generic.sh in there
> > - rename it my_rdf.sh (or something)
> > - create a file "csg_table" with a single line
> > rdf gromacs my_rdf.sh
> > in there. ("gromacs" should be replaced by the MD engine you are
> > planning to use.)
> > - add the path to the new folder to "scriptpath" option in your
> settings.xml
> > - modify my_rdf.sh to your needs
> >
> > Christoph
> >
> >>
> >> Christianna
> >>
> >> --
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> >
> >
> > --
> > Christoph Junghans
> > Web: http://www.compphys.de
> >
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Re: [votca] Hessian NOT a positive definite!

[Sikandar Mashayak]

Hi Andrey,

Sorry for the late reply. I am traveling so I could not reply sooner.

In regards to your question about discrepancies between CG-CG.param.init
and CG-CG.pot.new in Step_000, the difference is due to the definition of
the uniform cubic B-Spline functional form; see Eqs. 3.1 and 3.2 in Ref.
https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0131754#authcontrib
. CG-CG.param.init are considered as knot-values, c_{i}, for the B-Spline
form, which are not the same as the potential values, u_{i}. Therefore,
CG-CG.param.init and CG-CG.pot.new
 are not exactly the same.

For example, in your CG1-CG1.param.init file with uniform spacing, \Delta
r, of 0.02, for i = 26, r_i = 0.5, c_i = -3.3745224. If you evaluate u_i
for i = 26 using the above B-Spline form, you get u(r=0.5) = -3.351, which
is not same as c(r=0.5)= -3.3745224 given in the CG1-CG1.param.init. This
explains the difference between your CG-CG.param.init and CG-CG.pot.new
plots.

In regards to Hessian Not Positive Definite Error, first check the CG-CG
RDFs computed in the Step_000. These should be very close to those obtained
from IBI since your initial potential guess is from IBI. Could you please
check the RDFs in Step_000?

--
Sikandar



On Tue, Nov 20, 2018 at 3:28 AM 'Andrey Brukhno' via votca <
votca@googlegroups.com> wrote:

> Hi Sikandar,
>
> Sorry for the delay. Attached is the ZIP file containing the data:
>
> CG1-CG1.pot.in & CG1-CG2.pot.in - the original data obtained with IBI
> earlier;
> CG1-CG1.param.init & CG1-CG2.param.init - the above data interpolated onto
> coarser grid with cubic splines.
>
> I tried to run an RE iteration starting with the latter two files
> (actually 10 potentials in total) and using B-splines but ran into the
> systematic errors with csg_reupdate, as I reported previously.
>
> Thanks for looking into it.
> Andrey
>
> Below is a relevant extract from my settiings.xml (it is same for the
> second interaction):
> ---
>   
> 
> CG1-CG1
> 
> CG1
> CG1
> 
> 0
> 1.66
> 0.005
>   
> 
> cbspl
> 
> 84
> extrapolate
> 
>   
> 
>   
>   TCH-TCH.dist.tgt
>   
>   
>   1 0 0
>   
>   
>   smooth
>   
>   
> 
> 
>   3
> 
>   
>   
>   
>   acc_convergence average
>   
> 
> 
>   
>   pot
>   1.0
>   cur
>   2
> 
> 
>   param pot
> 
>   
>   
>   
> table_CG1_CG1.xvg
>   
> 
>   
>
> ---
>
>
> On Friday, November 16, 2018 at 6:49:21 PM UTC, sikandar wrote:
>>
>> Hi Andrey,
>>
>> Could you please send me the raw data of your plots?
>>
>> Thanks,
>> Sikandar
>>
>> On Tue, Nov 13, 2018 at 4:32 PM 'Andrey Brukhno' via votca <
>> vo...@googlegroups.com> wrote:
>>
>>> Hi Sikandar,
>>>
>>> I have tried different ranges and different number of knots in the
>>> initial data for CG-CG param.init files, yet I am getting obvious
>>> discrepancies between the data provided and the data generated by
>>> csg_reupdate for CG-CG.pot.new at the veryy beginning of the RE iteration,
>>> i.e. at step_000.
>>>
>>> Please check the new graph attached, exemplifying that the shifts along
>>> x-axis can be far from trivial (as opposed to what I thought before based
>>> on my first hands-on attempt). Clearly, the interpolated data (dashed
>>> lines) are not usable for a reliable RE iteration. I have 10 different
>>> potential types and all of them are skewed like that by csg_reupdate.
>>>
>>> I still hope that I am missing something which should be corrected in my
>>> input, and that it is not a typical interpolation behaviour with B-splines.
>>>
>>> Could you comment on this, please.
>>>
>>> Thanks
>>> Andrey
>>>
>>> On Monday, July 23, 2018 at 5:45:29 PM UTC+1, sikandar wrote:

 Hi Andrey,

 What do the lines in your plot correspond to? Are you plotting
 param.init vs the potential computed from them? If so, the knot values in
 parameter file and the potential are not the same. Please see Eq. 3.1 from
 http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0131754
 .

 Let me know if I missed anything.

 --
 Sikandar

 On Mon, Jul 23, 2018 at 9:11 AM Christoph Junghans 
 wrote:

> On Mon, Jul 23, 2018 at 9:28 AM, 'Andrey Brukhno' via votca
>  wrote:
> > Any comment on this "shift" issue?
> > I tried to find the relevant script in share/votca/scripts/inverse
> but it
> > seems that all interpolation is done by `csg_reupdate' app, and I
> didn't
> > have time up to now to look into the code.
> No idea, that is more a question for Sikandar!
>
> >
> > Thanks! / Andrey
> >
> > On Friday, July 20, 2018 at 11:59:37 AM UTC+1, Andrey Brukhno wrote:
> >>
> >> 

Re: [votca] Re: csg_reupdate error: property not found: re.function

[Sikandar Mashayak]

Hi Andrey,

In the case of non-bonded CG pair potentials, the AA ensemble average
values for dU/d\lambda and d^2U/d\lambda^2 are computed using the reference
AA pair correlations (i.e., CG-CG.dist.tgt). See Eq. 2.11 in
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0131754

--
Sikandar

On Wed, Aug 1, 2018 at 5:21 AM 'Andrey Brukhno' via votca <
votca@googlegroups.com> wrote:

> Hi Christoph & Sikandar,
>
> It's been a while since I asked the question below...
>
> On Monday, July 23, 2018 at 7:51:14 PM UTC+1, Andrey Brukhno wrote:
>>
>>
>> >>> Actually, I am a bit confused not seeing re.traj tag for atomistic
>>> >>> trajectory. I thought RE iteration requires recalculating CG
>>> averages in
>>> >>> over atomistic ensemble (trajectory) for every new set of CG
>>> potentials?
>>> >>>
>>> >>> Also, what about the corresponding re.topology tag - specifying what?
>>> >>
>>> >> Both options exist:
>>> >>
>>> >>
>>> https://github.com/votca/csg/blob/master/share/scripts/inverse/update_re.sh#L30
>>> >>
>>> >
>>> > Just to clarify: above you confirm that the two tags
>>> > `cg.inverse.$sim_prog.re.topol' and `cg.inverse.$sim_prog.re.traj'
>>> specify
>>> > the tpr and xtc/trr files for the original fine-detail (atomistic)
>>> > simulation?
>>> No these are just options, which allow you to overwrite the
>>> coarse-grained topology and trajectory.
>>> Nothing atomistic here!
>>
>>
>
>
>> If so, I am back to my question of how are the averages over fine detail
>> (atomistic) ensemble calculated for a new CG model/FF at each iteration?
>> I am referring to Eqs. 2.24 and 2.26 in the manual (page 8).
>>
>
> According to the equations each RE iteration should recalculate the
> averages corresponding to the "AA" (fine-detail) ensemble using a new CG
> representation (i.e. updated force-field), and this is what I fail to find
> in the tutorial for spce/re.
>
> Could you please clarify this.
>
> Andrey
>
>
>
>>
>>
>>>
>>> > For reference, below is the extract from
>>> `share/votca/xml/csg_defaults.xml',
>>> > where no traj tag is present (this is for v1.4.1, so perhaps in v1.5.1
>>> the
>>> > tag is there?):
>>> >
>>> >   
>>> >   
>>> > Special topology file to be used for
>>> > csg_reupdate
>>> >   
>>> >   
>>> >
>>> > Btw, my original question was: why these are not specified in
>>> `settings.xml'
>>> > in the (spce/re) case you referred to above?
>>> If they are not specified the default topology (topol.tpr) and default
>>> trajectory (traj.xtc) are used.
>>>
>>> >
>>> > Thanks / Andrey
>>> >
>>> >> Christoph
>>> >>
>>> >>>
>>> >>> Andrey
>>> >>>
>>> 
>>> 
>>> >>> --
>>>
>> --
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Re: [votca] Hessian NOT a positive definite!

[Sikandar Mashayak]

Hi Andrey,

What do the lines in your plot correspond to? Are you plotting param.init
vs the potential computed from them? If so, the knot values in parameter
file and the potential are not the same. Please see Eq. 3.1 from
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0131754 .

Let me know if I missed anything.

--
Sikandar

On Mon, Jul 23, 2018 at 9:11 AM Christoph Junghans 
wrote:

> On Mon, Jul 23, 2018 at 9:28 AM, 'Andrey Brukhno' via votca
>  wrote:
> > Any comment on this "shift" issue?
> > I tried to find the relevant script in share/votca/scripts/inverse but it
> > seems that all interpolation is done by `csg_reupdate' app, and I didn't
> > have time up to now to look into the code.
> No idea, that is more a question for Sikandar!
>
> >
> > Thanks! / Andrey
> >
> > On Friday, July 20, 2018 at 11:59:37 AM UTC+1, Andrey Brukhno wrote:
> >>
> >> ...
> >> As a matter of fact, the problem appears to be not a poor interpolation
> >> but a systematic shift in the X axis (by the size of the grid bin in the
> >> original data, i. e. param.init files) - see the corrected graph where I
> >> simply shifted all the interpolation curves by dx=0.02.
> >>
> >> So I conclude that something is fishy about the x column in the pot.cur
> >> files.
> >>
> >> Andrey
> >>
> >> On Friday, July 20, 2018 at 11:45:27 AM UTC+1, Andrey Brukhno wrote:
> >>>
> >>> Hi Christoph & Sikandar,
> >>>
> >>> Thank you both for your replies!
> >>>
> >>> Per your suggestions, I have compared the potentials generated (i.e.
> >>> B-spline interpolated) based on the initial guesses provided as
> >>> CGi-CGj.param.init files with the original data (i.e. the contents of
> those
> >>> param.init files). I found systematic discrepancies (see the attached
> graph,
> >>> where only 3 potentials shown)! - No wonder I am getting into trouble
> after
> >>> a new simulation with the potentials being that much off, especially at
> >>> shorter distances.
> >>>
> >>> Is it normal to have such large differences with the interpolated data?
> >>> I would think that there must be a way to improve on the interpolation
> by
> >>> varying something in the input - ?
> >>> Is it where the LJ repulsive core would help? (Although I think that
> >>> would be an ad hoc workaround for the poor interpolation issue.)
> >>>
> >>> It seems I still need your advice here, based on your practical
> >>> experience.
> >>>
> >>> Andrey
> >>>
> >>> On Friday, July 20, 2018 at 7:39:45 AM UTC+1, sikandar wrote:
> 
>  Hi Andrey,
> 
>  Below are some of the things you can try to address this issue.
> 
>  1. Make sure the potentials generated from your initial parameters are
>  physically consistent
>  2. Increase number of timesteps in CG simulation
>  3. Decrease the scaling parameter
>  4. If your CG system has charges, then you may need to add a LJ type
>  potential to your CBSPL CG potential after every CG update to ensure
> that
>  the CG potential is repulsive enough at short distances and does not
> allow
>  overlap of oppositely charged sites. You can enable this option by
>  specifying post_update block for every CG potential pair as
>  
>  ...
>  lj
>  
>  
>   LJ C6 Value 
>   LJ C12 Value 
>  
>  
>  ...
>  
> 
>  I hope this helps.
> 
>  Best,
>  Sikandar
> 
>  On Thu, Jul 19, 2018 at 6:13 PM Christoph Junghans  >
>  wrote:
> >
> >
> >
> > On Thu, Jul 19, 2018 at 18:15 'Andrey Brukhno' via votca
> >  wrote:
> >>
> >> Hello,
> >>
> >> I managed to run the RE iteration for a system with 10 non-bonded
> >> potentials (types).. well, the first iteration anyway, where it
> terminated
> >> after about an hour of running csg_reupdate with the following
> error:
> >>
> >> Hessian NOT a positive definite!
> >> This can be a result of poor initial guess or ill-suited CG
> potential
> >> settings or poor CG sampling.
> >>
> >> My understanding is, sometimes this might happen, but this was my
> >> second trial where I virtually doubled (44 -> 88) the number of
> knots and
> >> (in both cases) I use potentials derived from an earlier IBI
> iteration.
> >>
> >> I would really appreciate clues, hints or general advice as to how
> to
> >> alleviate the issue.
> >
> > Sikandar will know more, but most likely you will need to throw away
> > some frames at the beginning of the trajectory and run the
> iterations for a
> > bit longer!
> >
> > Christoph
> >>
> >>
> >> Thanks!
> >> Andrey
> >>
> >> --
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> 

Re: [votca] Re: Initial parameters for RE iteration with 10 potentials

[Sikandar Mashayak]

Hi Andrey,

The initial parameter file *.param.init for the B-spline potential function
contains break-points in the first column and knot values in the second
column.

As you observed in csg-tutorial/spce/re/ example, the initial values for
the knot values can be set to the PMF obtained by inverting the target
RDFs, i.e., c_i = -kTlog(g(r_i)). I have found this approach of
initializing knot values work well in my RE coarse-graining experiments.

Best,
Sikandar

On Wed, Jul 18, 2018 at 4:42 PM 'Andrey Brukhno' via votca <
votca@googlegroups.com> wrote:

> Well, to reduce the burden on the developers' answering (probably obvious
> for them) questions, here is what I discovered by simply plotting the
> CG-CG.param.init file from the tutorial in csg-tutorials/spce/re/
>
> The CG-CG.param.init file appears to contain the -RT\ln(g_{target}(r))
> data sampled at the spline knots, i.e. the first column is for the knot
> values (r) and the second column is the corresponding PMF in kJ/mol - see
> the attached plot. I am not sure what is the origin for the slight
> discrepancies that are seen in the graph (resampling artefacts?), but it
> seems that the mystery about this file has been cleared up.
>
> Andrey
>
> On Wednesday, July 18, 2018 at 10:23:27 PM UTC+1, Andrey Brukhno wrote:
>>
>> Wow, nobody can answer this straightaway? - I wonder: does this mean that
>> no non-associate of the VOTCA team ever used RE method for their actual
>> problem (i.e. not a tutorial case)?
>>
>> Anyway, may I ask those on the team now: in what relation VOTCA's
>> B-spline definition is with the corresponding Sci-Py class
>> (scipy.interpolate.BSpline)?
>>
>>
>> https://docs.scipy.org/doc/scipy/reference/generated/scipy.interpolate.BSpline.html
>>
>> I also have another question: what is the actual format of the
>> .param.init file? - it is far from being clear in the manual, as the file
>> itself is never described.
>>
>> Thanks again.
>>
>> Andrey
>>
>> On Wednesday, July 18, 2018 at 6:51:44 PM UTC+1, Andrey Brukhno wrote:
>>>
>>> Hello,
>>>
>>> In an attempt to compare some data obtained with IBI to RE, I am trying
>>> to start a relative entropy iteration for the same system. However, I do
>>> not know how to generate the initial parameters (aka CG-CG.param.init file)
>>> for my system (which would comprise 10 different interaction types).
>>>
>>> Initially I thought VOTCA would be able to generate the necessary
>>> *.param.init files based on my initial potentials provided as *.pot.in
>>> (the IBI results) and/or distributions (*.dist.tgt). But it seems not to be
>>> the case, as it complaints in the inverse.log about missing *.param.init
>>> files.
>>>
>>> Can anyone suggest a workaround? - I googled and searched here but did
>>> not find anything regrading a practical way of creating those files (nor in
>>> the manual).
>>>
>>> Please note: my question is very practical - I know how fit numerical
>>> data with regular cubic splines, say in Grace, but VOTCA is using B-splines
>>> which are more general (which is good!) but also more involved, so I guess
>>> the coefficients of cubic splines cannot be used as initial "guess" for the
>>> RE iteration.
>>>
>>> I essentially need to know what software could do that - ?
>>>
>>> Thanks in advance!
>>>
>>> Andrey
>>>
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Re: [votca] VOTCA protein

[Sikandar Mashayak]

Daniel,

In regards to extending relative entropy implementation in VOTCA, it is
possible but not trivial. Hybrid approach of BI for bonded and Relative
entropy for non-bonded can work. So as a starting point, you can use BI for
bonded interaction. For extending relative entropy implementation to bonded
interactions, see the current implementation in csg source code at
src/tools/csg_reupdate.cc . Mainly you would need to implement function
void CsgREupdate::AAavgBonded(PotentialInfo* potinfo) . There other things
also you need to take care regarding reading, writing bond interaction
parameters, and generating bond interaction tables for CG MD simulations.

Thanks,
Sikandar



On Thu, Feb 1, 2018 at 10:12 AM, Christoph Junghans 
wrote:

> On Wed, Jan 31, 2018 at 11:14 AM, Adiran  wrote:
> >
> >
> > El miércoles, 31 de enero de 2018, 15:30:03 (UTC), Christoph Junghans
> > escribió:
> >>
> >> On Wed, Jan 31, 2018 at 3:50 AM,   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.
>
> Also sec Section 2.2.1 of the manual 
> >
> > 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.
>
> >
> >
> >
> >>
> >>
> >> >
> >> > 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?
>
> 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 

Re: [votca] VOTCA protein

[Sikandar Mashayak]

Hi Daniel,

Are you running the spce/re entropy tutorial? Please make sure GSL library
is linked properly, sometimes there is an issue in linking to GSL due to
which relative entropy update fails.

--
Sikandar

On Wed, Jan 31, 2018 at 11:14 AM, Adiran  wrote:

>
>
> El miércoles, 31 de enero de 2018, 15:30:03 (UTC), Christoph Junghans
> escribió:
>>
>> On Wed, Jan 31, 2018 at 3:50 AM,   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 <
>> jung...@votca.org>
>> >> wrote:
>> >>>
>> >>> 

Re: [votca] VOTCA protein

[Sikandar Mashayak]

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. 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

---
Sikandar



On Tue, Jan 30, 2018 at 10:26 AM, Christoph Junghans 
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.
>
> Christoph
>
> On Tue, Jan 30, 2018 at 5:17 AM,   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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Re: [votca] relative entropy with lj126 interactions

[Sikandar Mashayak]

Hi Tom,

You can provide initial guess for LJ interaction parameters for relative
entropy as

#x y
0 1.0e-6
1 1.0e-3

where first y value corresponds to C12 and second y value corresponds to C6.

Cheers,
Sikandar

On Fri, Sep 29, 2017 at 7:55 AM, Tom  wrote:

>
> Hi,
>
> I want to use relative entropy method with Lennard-Jones interactions.
> What is the correct file format for the *.param.init file?
>
> Thanks,
> Tom
>
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Re: [votca] gmx topology reader

[Sikandar Mashayak]

Thanks Christoph.

On Sun, Aug 27, 2017 at 6:16 PM, Christoph Junghans <jungh...@votca.org>
wrote:

> My mistake, fixed:
> https://github.com/votca/csg/commit/d44eb32ebbfdafd6e8c5a174df142f
> 969ccaf489
>
> 2017-08-27 14:35 GMT-06:00 Sikandar Mashayak <symasha...@gmail.com>:
> > Hi,
> >
> > Its not clear why gmx topology reader is printing "cout << "XXX: " <<
> > a->resind << endl;"
> >
> > --
> > Sikandar
> >
> > --
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>
>
>
> --
> Christoph Junghans
> Web: http://www.compphys.de
>
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[votca] gmx topology reader

[Sikandar Mashayak]

Hi,

Its not clear why gmx topology reader is printing "cout << "XXX: " <<
 a->resind << endl;"

--
Sikandar

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Re: [votca] Re: Issues with a charged molecule

[Sikandar Mashayak]

Hi Romnik,

As you know, force-matching tries to match the total force on the CG beads
from CG force field with that from the reference atomistic simulations.

In your CG system, there are two components of the CG force field, first
from the electrostatic interactions due to charges on the counterion and
dye molecule and second from the vdW CG potentials.

Therefore, in force-matching the objective is to

force from electrostatics with CG topology + force from CG vdW potentials =
total force from reference atomistic simulations.

Since, csg_fmatch optimizes only the vdW component of the CG potentials,
the target force to the force-matching should be

force from CG vdW potentials = total force from reference atomistic
simulations - force from electrostatics with CG topology

One thing to note here is that the electrostatic forces with CG topology
will not be same as the electrostatic forces in atomistic trajectories.
Therefore, to compute electrostic forces in the CG system, you should
perform -rerun with CG trajectory and force field itp file for CG system
with vdW parameters set to zero. Moreover, you are coarse-graining water
molecules into a neutral CG bead, so it won't be able to capture
dielectric/polarization effects of water on the electrostatic interactions
among charged beads. So you will need to explicitly specify some dielectric
constant (such as 78.5) while determining electrostatic interactions in CG
system.

I hope with this approach you should be able to find meaningful values for
CG potentials.

Best,
Sikandar


On Thu, Mar 23, 2017 at 5:28 AM, Rom  wrote:

> Thanks guys!
>
> I tried using a larger minimum on many different mapping systems etc, even
> completely different simulations, and it still has the same issue.
>
> I have attached a compressed file with my .xml mapping files, where
> str.xml = dye structure
> cou.xml = counterion
> sol.xml = water solvent
>
> index_62_5.ndx = index file for when i perform a rerun
>
> topology file I use for my rerun, along with the .itp file for each.
>
>
> On Wednesday, 22 March 2017 11:55:15 UTC, Rom wrote:
>>
>> Hi all :)
>>
>> I am working on a system where I have a large charged dye molecule, a
>> charged counterion, and water as the solvent.
>>
>> The atomistic simulations are good, and yet when i force match the
>> interactions, any interaction with the counterion (counterion-counterion,
>> dye-counterion etc) all show a force profile of peaks and wells at around
>> 10^13 and 10^-13!
>> I thought maybe it was the -rerun part, so I deleted all the charges in
>> my topology before re-running, since i thought it was the charge that was
>> an issue, and yet it is still doing this!
>>
>> Does anyone know what the problem is? Is there a certain way to deal with
>> charged molecules when force matching?
>>
>> Many thanks!
>> Romnik
>>
>> p.s. if you need to look at any files, just let me know so I can attach
>> them
>>
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Re: [votca] Issues with a charged molecule

[Sikandar Mashayak]

Hi Romnik,

One simple thing you could try is increase the min distance in the options
file and see if that helps.

There could be other issues depending upon how you coarse-grain the water
molecules and how you assign the charges in the CG topology. If you could
please send us the input files, I would be able to better answer this issue.

Thanks,
Sikandar

On Wed, Mar 22, 2017 at 2:30 PM, Christoph Junghans 
wrote:

> 2017-03-22 5:55 GMT-06:00 Rom :
> > Hi all :)
> >
> > I am working on a system where I have a large charged dye molecule, a
> > charged counterion, and water as the solvent.
> >
> > The atomistic simulations are good, and yet when i force match the
> > interactions, any interaction with the counterion (counterion-counterion,
> > dye-counterion etc) all show a force profile of peaks and wells at around
> > 10^13 and 10^-13!
> > I thought maybe it was the -rerun part, so I deleted all the charges in
> my
> > topology before re-running, since i thought it was the charge that was an
> > issue, and yet it is still doing this!
> >
> > Does anyone know what the problem is? Is there a certain way to deal with
> > charged molecules when force matching?
> That is more a question for Sikandar
>
> >
> > Many thanks!
> > Romnik
> >
> > p.s. if you need to look at any files, just let me know so I can attach
> them
> >
> > --
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>
>
>
> --
> Christoph Junghans
> Web: http://www.compphys.de
>
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Re: [votca] Re: Pressure Correction LAMMPS

[Sikandar Mashayak]

On Thu, Feb 16, 2017 at 2:23 PM, Christoph Junghans 
wrote:

> 2017-02-16 13:05 GMT-07:00 Joshua Moore :
> > Hi Christoph,
> >
> > Thanks again.  I think I've implemented all your suggestions except for
> >
> > "If you want to allow a pressure file per-interaction add
> >  to  block inside the  block
> > and use
> > p_file="$(csg_get_interaction_property inverse.lammps.pressure_file)" "
> >
> > I will have to think about that one.  I think just a single pressure
> makes
> > sense, no?
> Multi-component pressure correction is bit tricky. You would need the
> contribution from each individual interaction.
> The standard version of Gromacs cannot calculated that and hence we
> just use the total pressure.
>

Won't this cause extra counting/corrections to the multiple interactions,
i.e., multiple pair potentials will be modified to correct the same
pressure resulting in over corrections and hence, error.

I think, either the pressure correction should be added to only one
interaction for a given iteration or use partial pressures corresponding to
each interaction to compute the pressure corrections.

Best,
Sikandar


> You could also do a version where it fails back to total pressure,
> something like:
>  p_file="$(csg_get_interaction_property --allow-empty
> inverse.lammps.pressure_file)"
> [[ -z ${p_file] ]] && p_file="$(csg_get_interaction_property
> inverse.lammps.pressure_file)"
>
> One more thing, please add documentation for new xml options to
> share/xml/csg_defaults.xml.
>
> >
> > The other issue was a typo.  Thanks for suggesting that.  I had
> >  in twice, the second time, with nothing in
> it,
> > so think it overrides the previous block.  Seems to be updating now.
> Good that you found it, I have seen that problem before!
>
> Christoph
> >
> > I will do a pull request later today after a bit more testing, but I
> think
> > it's ok now.
> >
> > Thanks.
> >
> > Josh
> >
> >
> >
> > On Thursday, February 16, 2017 at 1:46:29 PM UTC-5, Christoph Junghans
> > wrote:
> >>
> >> 2017-02-16 10:20 GMT-07:00 Joshua Moore :
> >> > Hi Christoph,
> >> >
> >> > I think I have it basically working now, but I might be having a few
> >> > issues.
> >> > Here is what I did
> >> >
> >> > 1) I created a calc_pressure_lammps.sh file as you suggested.  It is
> >> > attached, but it is basically just calculating the average of a column
> >> > of
> >> > pressures I've outputted from LAMMPS using awk and assigning this to
> the
> >> > p_new variable.  I have hard coded the name of the lammps file (called
> >> > lammps.pressure), as I wasn't sure how this could be read into the
> >> > script.
> >> Nice, it looks very good!
> >>
> >> I would add an option to xml file in lammps block, e.g.
> >> 
> >>   ...
> >>   
> >>
> >>   ...
> >>   traj.dump
> >>   ...
> >>   lammps.pressure
> >> 
> >>   
> >> 
> >> and then you can read its value inside the script using:
> >> p_file="$(csg_get_property cg.inverse.lammps.pressure_file)"
> >> If you want to allow a pressure file per-interaction add
> >>  to  block inside the  block
> >> and use
> >> p_file="$(csg_get_interaction_property inverse.lammps.pressure_file)"
> >>
> >> In addition, I would check if the pressure file exists before invoking
> >> awk:
> >> [[ -f ${p_file} ]] || die "${0##*/}: pressure file '${p_file}" doesn't
> >> exist"
> >> and check that awk actually ran correctly:
> >> p_now=$(...) || die "${0##*/}: pressure averaging failed"
> >>
> >> (Note "${0##*/}" is just the name of the script)
> >> >
> >> > 2)
> >> > Added "pressure lammps calc_pressure_lammps.sh" in csg_table below
> >> > "pressure
> >> > gromacs calc_pressure_gromacs.sh"
> >> >
> >> > 3) Commented out in postupd_pressure.sh this line
> >> >
> >> > #[[ $sim_prog != gromacs ]] && die "${0##*/}: pressure correction for
> >> > ${sim_prog} is not implemented yet!"
> >> I would change it to that:
> >> [[ $sim_prog != @(gromacs|lammps) ]] && die "${0##*/}: pressure
> >> correction for ${sim_prog} is not implemented yet!"
> >> so that it only works for lammps and gromacs
> >>
> >> Can you do a pull request with these changes?
> >> Details:
> >>  contribute-a-bug-fix>
> >>
> >> >
> >> > 4) It seems to be running and the pressure appears to be improving.  I
> >> > have
> >> > 3 bead types for the hexane example, and 3 interactions, A-A, B-B, and
> >> > A-B.
> >> > VOTCA is only writing a A-A.pressure and a A-B.pressure file.  It
> >> > doesn't
> >> > seem to be writing a B-B.pressure file, so I'm not sure if it is
> >> > updating
> >> > the B-B interaction??
> >> That is a bit more tricky. I am guessing there is a typo in the xml
> >> file, but I will look more in detail later.
> >> I would look for the output and check:
> >> - if the IBI update itself done for A-B
> >> - if pressure is listed as a Post-update for the A-B interaction
> >> - check inverse.log if 

Re: [votca] Error in Installation

[Sikandar Mashayak]

Yes boost 1.58 worked for me.

On Thu, Feb 2, 2017 at 7:07 AM, Christoph Junghans <jungh...@votca.org>
wrote:

> 2017-02-02 0:29 GMT-05:00 Sikandar Mashayak <symasha...@gmail.com>:
> > Hi Christoph,
> >
> > Here is the tools build error message with boost-1.14.1 and gcc 4.9.2, I
> > also tried gcc 4.7.1 which results in the same error.
> Wasn't Alireza's error ("undefined reference to
> `boost::program_options") a different issue?
>
> >
> > cd /home/mashaya1/Apps/votca/build/tools/src/libtools &&
> > /usr/local/software/GCC/4.9.2/bin/c++   -Dvotca_tools_EXPORTS -O3
> -DNDEBUG
> > -fPIC -I/home/mashaya1/Apps/votca/src/tools/include
> > -I/home/mashaya1/Apps/votca/build/tools/include -I/usr/local/include
> > -I/home/mashaya1/Apps/votca/build/tools/src/libtools-o
> > CMakeFiles/votca_tools.dir/linalg.cc.o -c
> > /home/mashaya1/Apps/votca/src/tools/src/libtools/linalg.cc
> > /home/mashaya1/Apps/votca/src/tools/src/libtools/linalg.cc: In function
> > 'double votca::tools::linalg_traceofProd(const
> > boost::numeric::ublas::matrix&, const
> > boost::numeric::ublas::matrix&)':
> > /home/mashaya1/Apps/votca/src/tools/src/libtools/linalg.cc:169:48:
> error:
> > invalid initialization of reference of type 'const
> > boost::numeric::ublas::vector&' from expression of type 'const
> > array_type {aka const boost::numeric::ublas::unbounded_array<double,
> > std::allocator >}'
> > const ub::vector& Aarray=A.data();
> > ^
> > /home/mashaya1/Apps/votca/src/tools/src/libtools/linalg.cc:170:48:
> error:
> > invalid initialization of reference of type 'const
> > boost::numeric::ublas::vector&' from expression of type 'const
> > array_type {aka const boost::numeric::ublas::unbounded_array<double,
> > std::allocator >}'
> > const ub::vector& Barray=B.data();
> I guess boost-1.41.1 is too old then, which version worked for you? 1.58?
> There is also the problem that not all gcc and boost combination work
> together.
>
> >
> > On Wed, Feb 1, 2017 at 6:48 AM, Christoph Junghans <jungh...@votca.org>
> > wrote:
> >>
> >> 2017-01-31 17:25 GMT-05:00 Sikandar Mashayak <symasha...@gmail.com>:
> >> > Hi,
> >> >
> >> > In the case of buildtb.log, the errors seem to be caused by Boost
> 1.41.0
> >> > library, however, if you build with later versions of Boost, e.g.,
> >> > 1.58.0,
> >> > build is successful. @ Christoph, is this expected from Boost 1.41.0?
> >> boost-1.14.1 is very old (2009), but should be fine. However the gcc
> >> is 4.9.2 (rather new) and it might be the combination of both.
> >>
> >> Alireza,
> >>
> >> 1.) if you have multiple versions of gcc and boost on the cluster, try
> >> different combinations.
> >> 2.) Plus, I updated build.sh to log stderr as well, so could you
> >> download the latest version (build.sh v2.1.3) and reproduce the error
> >> in an empty directory and send us that log, too.
> >>
> >> Christoph
> >>
> >> >
> >> > Thanks,
> >> > Sikandar
> >> >
> >> > On Tue, Jan 31, 2017 at 3:48 PM, Alireza Moradzadeh <
> a.mr...@gmail.com>
> >> > wrote:
> >> >>
> >> >> I attached the files.
> >> >>
> >> >>
> >> >> Best Regards,
> >> >> Alireza Moradzadeh
> >> >>
> >> >>
> >> >> On Tue, Jan 31, 2017 at 3:23 PM, Christoph Junghans
> >> >> <jungh...@votca.org>
> >> >> wrote:
> >> >>>
> >> >>> 2017-01-31 15:55 GMT-05:00 Alireza Moradzadeh <a.mr...@gmail.com>:
> >> >>> > I am trying to install in a cluster, which I previously worked and
> >> >>> > on
> >> >>> > another Supercomputer. I attach both error file from CMakeFiles.
> >> >>> Unfortunately, the files in CMakeFiles have very little useful
> >> >>> information.
> >> >>> I need the full output of build.sh use:
> >> >>> $ ./build.sh --verbose --log build.log tools
> >> >>> and send the build.log.
> >> >>> Plus, the CMakeCache.txt from tools would be nice, too.
> >> >>>
> >> >>> Christoph
> >> >>> >
> >> >>> >
> >> >>> > B

Re: [votca] Error in Installation

[Sikandar Mashayak]

Hi,

In the case of buildtb.log, the errors seem to be caused by Boost 1.41.0
library, however, if you build with later versions of Boost, e.g., 1.58.0,
build is successful. @ Christoph, is this expected from Boost 1.41.0?

Thanks,
Sikandar

On Tue, Jan 31, 2017 at 3:48 PM, Alireza Moradzadeh 
wrote:

> I attached the files.
>
>
> Best Regards,
> Alireza Moradzadeh
>
>
> On Tue, Jan 31, 2017 at 3:23 PM, Christoph Junghans 
> wrote:
>
>> 2017-01-31 15:55 GMT-05:00 Alireza Moradzadeh :
>> > I am trying to install in a cluster, which I previously worked and on
>> > another Supercomputer. I attach both error file from CMakeFiles.
>> Unfortunately, the files in CMakeFiles have very little useful
>> information.
>> I need the full output of build.sh use:
>> $ ./build.sh --verbose --log build.log tools
>> and send the build.log.
>> Plus, the CMakeCache.txt from tools would be nice, too.
>>
>> Christoph
>> >
>> >
>> > Best Regards,
>> > Alireza Moradzadeh
>> >
>> >
>> > On Tue, Jan 31, 2017 at 1:04 PM, Christoph Junghans > >
>> > wrote:
>> >>
>> >> 2017-01-31 13:49 GMT-05:00 Alireza Moradzadeh :
>> >> > I am using boost/1.51.0. Basically, I exactly repeat instruction in
>> the
>> >> > handout.
>> >> What version of VOTCA?
>> >> And is this a fresh checkout?
>> >> Can you attach the full output of build.sh?
>> >>
>> >> Christoph
>> >>
>> >> Christoph
>> >> > Thanks,
>> >> > Alireza
>> >> >
>> >> > On Tuesday, January 31, 2017 at 7:58:24 AM UTC-6, Christoph Junghans
>> >> > wrote:
>> >> >>
>> >> >> 2017-01-30 20:33 GMT-05:00 Alireza Moradzadeh :
>> >> >> > Dear VOTCA Users,
>> >> >> >
>> >> >> > I get an error in installation of votca, any solution is highly
>> >> >> > appreicated.
>> >> >> Which version of boost are you using? Which version of VOTCA are you
>> >> >> trying to build?
>> >> >> And did you build from scratch? (Otherwise try a fresh checkout or
>> the
>> >> >> build.sh options "--clean-out" or "--clean-ignored")
>> >> >>
>> >> >> Christoph
>> >> >> >
>> >> >> > Thanks,
>> >> >> > Alireza
>> >> >> >
>> >> >> > Scanning dependencies of target votca_property
>> >> >> > [ 97%] Building CXX object
>> >> >> > src/tools/CMakeFiles/votca_property.dir/votca_property.cc.o
>> >> >> > Linking CXX executable votca_property
>> >> >> > CMakeFiles/votca_property.dir/votca_property.cc.o: In function
>> >> >> >
>> >> >> >
>> >> >> > `boost::program_options::validation_error::validation_error(
>> boost::program_options::validation_error::kind_t,
>> >> >> > std::string const&, std::string const&, int)':
>> >> >> >
>> >> >> >
>> >> >> > votca_property.cc:(.text._ZN5boost15program_options16validat
>> ion_errorC2ENS1_6kind_tERKSsS4_i[_ZN5boost15program_
>> options16validation_errorC5ENS1_6kind_tERKSsS4_i]+0x21):
>> >> >> > undefined reference to
>> >> >> >
>> >> >> >
>> >> >> > `boost::program_options::validation_error::get_template(
>> boost::program_options::validation_error::kind_t)'
>> >> >> >
>> >> >> >
>> >> >> > votca_property.cc:(.text._ZN5boost15program_options16validat
>> ion_errorC2ENS1_6kind_tERKSsS4_i[_ZN5boost15program_
>> options16validation_errorC5ENS1_6kind_tERKSsS4_i]+0x39):
>> >> >> > undefined reference to
>> >> >> >
>> >> >> >
>> >> >> > `boost::program_options::error_with_option_name::error_with_
>> option_name(std::string
>> >> >> > const&, std::string const&, std::string const&, int)'
>> >> >> > CMakeFiles/votca_property.dir/votca_property.cc.o: In function
>> >> >> >
>> >> >> >
>> >> >> > `boost::program_options::error_with_option_name::~error_
>> with_option_name()':
>> >> >> >
>> >> >> >
>> >> >> > votca_property.cc:(.text._ZN5boost15program_options22error_
>> with_option_nameD2Ev[_ZN5boost15program_options22err
>> or_with_option_nameD5Ev]+0x12):
>> >> >> > undefined reference to `vtable for
>> >> >> > boost::program_options::error_with_option_name'
>> >> >> > CMakeFiles/votca_property.dir/votca_property.cc.o: In function
>> >> >> > `boost::program_options::validation_error::~validation_error()':
>> >> >> >
>> >> >> >
>> >> >> > votca_property.cc:(.text._ZN5boost15program_options16validat
>> ion_errorD2Ev[_ZN5boost15program_options16validation_errorD5Ev]+0x12):
>> >> >> > undefined reference to `vtable for
>> >> >> > boost::program_options::error_with_option_name'
>> >> >> > CMakeFiles/votca_property.dir/votca_property.cc.o: In function
>> >> >> >
>> >> >> > `boost::program_options::invalid_option_value::~invalid_
>> option_value()':
>> >> >> >
>> >> >> >
>> >> >> > votca_property.cc:(.text._ZN5boost15program_options20invalid
>> _option_valueD2Ev[_ZN5boost15program_options20inv
>> alid_option_valueD5Ev]+0x12):
>> >> >> > undefined reference to `vtable for
>> >> >> > boost::program_options::error_with_option_name'
>> >> >> > CMakeFiles/votca_property.dir/votca_property.cc.o: In function
>> >> >> >
>> >> >> >
>> >> >> > `boost::program_options::error_with_option_name::~error_
>> 

Re: [votca] Relative entropy - long range Coulomb pressure

[Sikandar Mashayak]

Hi,

As Christoph suggested, read in the file and store time series of energy
values into an array (or table data type). First verify the accuracy of the
implementation in a serial version of the code.

The multi-threaded parallel version of relative entropy is handled for
CsgREupdateWorker class. So, for the parallel version, you need to define a
similar variable to store time series data of Coulomb energy in the
CsgREupdateWorker class and initialize in the ForkWorker function.

Different threads process different set of frames in the parallel version
of the code. So you need to access appropriate value (index) in the Coulomb
energy array consistent with the time step of the frame being processed by
the thread. This can be achieved by querying the time step of the frame the
thread is processing in CsgREupdateWorker::EvalConfiguration via getStep()
function and then appropriately reading the value from the Coulomb energy
array.

I hope above explanation helps. Let me know if you need more clarification
or details.

Cheers,
Sikandar

On Tue, Jan 31, 2017 at 7:04 AM, Christoph Junghans 
wrote:

> 2017-01-30 8:00 GMT-05:00 Mohammad Motevaselian  >:
> > Hi,
> >
> > I am trying to implement long range Coulomb contribution to the
> pressure. I
> > do not want to calculate this in a direct way ( short range
> electrostatic +
> > PME), rather
> > I use Gromacs to give the Coulomb energy and devide it by the 3*V. For
> this
> > purpose, I store the Coulomb energy vs number of frames in a file, say
> > ucol.new, in each step of the CG.
> >
> > My question is :
> >
> > Any time dependent quantity in the csg_reupdate will be distributed among
> > the workers ( threads) and subsequently their results will be merged. I
> was
> > wondering
> > how can I be sure that the data in my file "ucol.dat" will be used
> correctly
> > in the calculations?
> First of all, I would start with a serial version.
> I think you need add an option specifying the file and then read it in
> BeginEvaluate().
>
> Sikandar as you wrote csg_reupdate, please correct me if I am wrong.
>
> Christoph
> >
> > I would appreciate it if anyone can help me with this.
> > Please let me know if you want any further explanation regarding my
> > question.
> >
> > Thanks a lot,
> > Mohammad
> >
> > --
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> > "votca" group.
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> > email to votca+unsubscr...@googlegroups.com.
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> > 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
>
> --
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Re: [votca] Adding a new C function in csg/src/tool/ in VOTCA

[Sikandar Mashayak]

Hi,

The reason, I do not compute running sum of  by inside the
EvalNonBonded

_dUFrame(row) += dU_i

 is to avoid double computations of first derivatives required to compute
 part of the Hessian matrix.

So as long as you appropriately take care of  components of the
Hessian, your approach would also work. But it would require double
computations of U_i.

Best,
Sikandar

On Fri, Nov 4, 2016 at 4:09 PM, Mohammad Motevaselian <
h.motevasel...@gmail.com> wrote:

> Thanks Sikandar, I think I will try the first option for now.
>
> I went through the relative entropy code to understand its code structure,
> since I want to use some of its functions,
> and I have the following question:
>
> The EvalNonbonded function in csg_reupdate.cc takes in only one
> interaction information, and that's why you defined "_dUFrame"
> to construct a nlamda by 1 matrix for the first derivative of U w.r.t
> potential parameters. And then, since you want the  you reset
> _dUFrame.clear() in EvalConfiguration and do the following running sum
> over the frames:
>
> _DS(row) += _dUFrame(row);
>
> My question is that can we do the following in the EvalNonbonded:
>
> _dUFrame(row) += dU_i ;
>
> And the would  _dUFrame(row) /= _nframes be equal  ?
>
> Please let me know if I am missing something?
>
> Thanks,
> Hossein
>
>
>
>
>
> On Friday, November 4, 2016 at 11:15:21 AM UTC-5, sikandar wrote:
>>
>> Hi,
>>
>> Currently VOTCA supports multi-thread parallel computations on single
>> node only using shared memory parallel implementation. It exploits trivial
>> parallelism in processing the frames in the MD trajectory. Since each frame
>> can be processed independently of other frames, total number of frames are
>> divided among the threads and at the end partial results from all the
>> threads are gathered to compute total quantities.
>>
>> To run VOTCA across multiple nodes, you need to implement distributed
>> memory based parallel computations using MPI. There are two options
>>
>> (i) use the similar frame based parallel computations where the frames
>> are now divided not only among threads but also among different nodes. This
>> should be easy to implement with basic MPI.
>>
>> (ii) domain decomposition where particles are distributed among different
>> nodes and pair potentials and force computations are done in parallel. This
>> is similar to what MD engine uses and not trivial to implement.
>>
>> I believe option (i) would be helpful if you have too many frames, which
>> is usually not the case for coarse-graining as for CG relatively short
>> trajectories are used for optimization.
>>
>> Best,
>> Sikandar
>>
>>
>>
>>
>>
>> On Thu, Nov 3, 2016 at 9:54 PM, Mohammad Motevaselian <
>> h.motev...@gmail.com> wrote:
>>
>>> Thank you Christoph, now I was able to add and compile my program in
>>> VOTCA.
>>> I have another question, when I use any coarse graining method in VOTCA,
>>> it only utilizes the existing number of threads of a core. If I am
>>> correct I cannot use multiple cores (like mpi) to run any VOTCA csg
>>> programs. I was wondering if there is any way to do that or
>>> it needs to be implemented in VOTCA?
>>>
>>> On Wednesday, November 2, 2016 at 6:40:32 PM UTC-5, Christoph Junghans
>>> wrote:

 2016-11-02 17:12 GMT-06:00 Mohammad Motevaselian :

 > Hi,
 >
 > So far I have worked with VOTCA to do coarse graining and went
 through the
 > structure of the codes and scripts (specifically csg_reupdate.cc and
 > csg_fmatch.cc).
 > I want now to implement a new C function in VOTCA. Could you please
 tell me,
 > where should I specify the name of my new function, such that cmake
 > understand
 > that it exists and compile it.
 All file named *.cc get compile into , e.g.
 csg_stat.cc  csg_stat_imc.cc  csg_stat_imc.h get compile into csg_stat.
 After adding the file to  csg/src/tools you need to re-run cmake.

 If you need a function in two csg programs, you need to add the file
 to libcsg (dir csg/src/libcsg) and rerun cmake.

 Christoph
 >
 > thanks
 > Mohammad
 >
 > --
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 Groups
 > "votca" group.
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 > email to votca+un...@googlegroups.com.
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 > For more options, visit https://groups.google.com/d/optout.



 --
 Christoph Junghans
 Web: http://www.compphys.de

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Re: [votca] Adding a new C function in csg/src/tool/ in VOTCA

[Sikandar Mashayak]

Hi,

Currently VOTCA supports multi-thread parallel computations on single node
only using shared memory parallel implementation. It exploits trivial
parallelism in processing the frames in the MD trajectory. Since each frame
can be processed independently of other frames, total number of frames are
divided among the threads and at the end partial results from all the
threads are gathered to compute total quantities.

To run VOTCA across multiple nodes, you need to implement distributed
memory based parallel computations using MPI. There are two options

(i) use the similar frame based parallel computations where the frames are
now divided not only among threads but also among different nodes. This
should be easy to implement with basic MPI.

(ii) domain decomposition where particles are distributed among different
nodes and pair potentials and force computations are done in parallel. This
is similar to what MD engine uses and not trivial to implement.

I believe option (i) would be helpful if you have too many frames, which is
usually not the case for coarse-graining as for CG relatively short
trajectories are used for optimization.

Best,
Sikandar





On Thu, Nov 3, 2016 at 9:54 PM, Mohammad Motevaselian <
h.motevasel...@gmail.com> wrote:

> Thank you Christoph, now I was able to add and compile my program in
> VOTCA.
> I have another question, when I use any coarse graining method in VOTCA,
> it only utilizes the existing number of threads of a core. If I am
> correct I cannot use multiple cores (like mpi) to run any VOTCA csg
> programs. I was wondering if there is any way to do that or
> it needs to be implemented in VOTCA?
>
> On Wednesday, November 2, 2016 at 6:40:32 PM UTC-5, Christoph Junghans
> wrote:
>>
>> 2016-11-02 17:12 GMT-06:00 Mohammad Motevaselian :
>> > Hi,
>> >
>> > So far I have worked with VOTCA to do coarse graining and went through
>> the
>> > structure of the codes and scripts (specifically csg_reupdate.cc and
>> > csg_fmatch.cc).
>> > I want now to implement a new C function in VOTCA. Could you please
>> tell me,
>> > where should I specify the name of my new function, such that cmake
>> > understand
>> > that it exists and compile it.
>> All file named *.cc get compile into , e.g.
>> csg_stat.cc  csg_stat_imc.cc  csg_stat_imc.h get compile into csg_stat.
>> After adding the file to  csg/src/tools you need to re-run cmake.
>>
>> If you need a function in two csg programs, you need to add the file
>> to libcsg (dir csg/src/libcsg) and rerun cmake.
>>
>> Christoph
>> >
>> > thanks
>> > Mohammad
>> >
>> > --
>> > 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
>>
> --
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Re: [votca] Adding new functional form to potential function of Relative Entropy

[Sikandar Mashayak]

Hi Alireza,

Your approach seems correct. May be you made some mistake in your
potentialfunctionXXX.h and *.cc files. If you copy pasted some code from
other potentialfuctions files, then you must make sure to update the class
names, #ifdef statements to be consistent with potentialfuctionXXX class
name. I hope that resolves the issue.

Best,
Sikandar

On Sun, Jul 17, 2016 at 1:39 AM, Alireza Moradzadeh 
wrote:

> Dear All,
>
> I want to add a new functional form to RE, I can do it with replacing one
> of the current functional forms, but I prefer I want to know what files I
> should change:
> I already added potentialfunctionXXX.cc and potentialfunctionXXX.h. I also
> added potentialfunctionXXX.h to csg_reupdate.h and added if potentialname
> == XXX ucg = new potentialfunctionXXX(y,y,y)
> but when I try to make csg_reupdate gives me back the following error.
>
> expected type specifier befor potentialfunctionXXX( y,y,y)
>
> Any suggestion?
>
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Re: [votca] How to use one specific cmake version to start ./build.sh

[Sikandar Mashayak]

Hi Chaofu Wu,

Try running./build.sh with the following option

./build.sh --cmake /usr/local/cmake/bin/cmake

You can see various options possible for the the build script with
./build.sh --longhelp


Cheers,
Sikandar

On Tue, May 24, 2016 at 9:55 PM, Wu Chaofu  wrote:

> Dear users or developer of votca,
> To install the votca of the latest version, I have installed cmake-3.5.2
> into the directory /usr/local/cmake, which is not one default position. At
> the default position, there is the cmake-2.8.3. I ran the following command
> export PATH=$PATH:/usr/local/cmake/bin
> before I started ./build.sh. However, The build procedure stoped with a
> wrong message as follows
> CMake 2.8.11 or higher is required. You are running version 2.8.3.
> So my question is:
> How to use one specific cmake version (cmake-3.5.2) to start ./build.sh?
> Thanks a lot for any reply.
> Yours sincerely,
> Chaofu Wu
>
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Re: [votca] SIMPLEX

[Sikandar Mashayak]

Hi,

Currently RE implementation does not support constraint optimization. So
only way to ensure physically meaningful parameters (C12, C6 or sigma
epsilon) is to provide good initial guess, check other MD simulation
parameters such as cut-off, dielectric permittivity in case of charges, and
using small enough relaxation/mixing parameter.

Best,
Sikandar

On Sat, Apr 9, 2016 at 8:31 PM, Christoph Junghans 
wrote:

> 2016-04-09 16:38 GMT-06:00 Alireza Moradzadeh :
> > I looked at simplex tutorials. I don,t now why we need n+1 line,
> n+1 sets is a requirement of the simplex algorigtm, see our recent paper:
> 
> or
> 
> > furthermore, when i tried to run my settings.xml based on the a
> combination rule I got the error mentioning there is no parameters for
> > interaction between two beads. I am trying simplex on a four bead model
> so I don't have enough parameters to allocate for all of the
> > interaction.
> Like I said in my last email you need at least one parameter per
> interaction, you have 3 interactions and 4 parameters so you should be
> fine. However looking at the code, I think it could be rewritten to
> list this constraint.
>
> Christoph
> >
> >> On Apr 9, 2016, at 2:49 PM, Christoph Junghans 
> wrote:
> >>
> >> 2016-04-08 22:26 GMT-06:00 Alireza Moradzadeh :
> >>> By the way I would be glad if you could provide more information on
> how to
> >>> choose parameters initials
> >>> I could not find so much information on how I should choose those
> value or
> >>> even its organization
> >> Have a look at the methanol-water simplex tutorial there is a
> >> simplex.in file for each interaction.
> >> The values in there are given in the same order as in the xml file.
> >> You will need n+1 sets to start with (lines in simplex.in) These sets
> >> can be generated by randomly perturbing some values from a single set,
> >> which you got from e.g. fitting an IBI potential.
> >>
> >> Christoph
> >>
> >>>
> >>> Thanks,
> >>> Alireza
> >>>
> >>>
>  On Friday, April 8, 2016 at 10:21:23 PM UTC-5, Alireza Moradzadeh
> wrote:
> 
>  Thank you for your answer.
> 
>  I am also wondering if there is a way to keep eps and sigma positive
>  during simulation time. Because the optimization method is blind to
> physical
>  meaning of eps and sigma I got negative value using other methods in
> votca
>  package.
>  Is it possible to enforce this condition using this method or RE.
> Also is
>  there anyway in votca package to treat charge of beads as a variable
> during
>  simulation so I could control sigma and epsilon by variable charge.
> 
>  Thanks,
>  Alireza
> 
> 
> > On Friday, April 8, 2016 at 4:04:48 PM UTC-5, Christoph Junghans
> wrote:
> >
> > 2016-04-07 19:10 GMT-06:00 Alireza Moradzadeh :
> >> Dear VOTCA Users,
> >>
> >>
> >> For a system composed of two beads , I want to optimize pressure and
> >> interaction based on RDF but I want to stick to Lorentz-Berthelot
> >> combination rule. I want to know if I define my function as follows
> >> would it
> >> be right or not? and should I define pressure as target in each
> >> interaction.
> > Parameters are always global so, you should not list any parameter
> > twice, but you need to list at least one parameter for each
> > interaction.
> > e.g. list eps1 sig1 for CG1-CG1, eps2 for CG1-CG2 and sig2 for
> CG2-CG2
> >>
> >> CG1-CG1
> >> target rdf presssure
> >> function  4*eps1*[(sig1/x)**12-(sig1/x)**6]
> >> parmeters eps1 sig1
> >>
> >> CG1-CG2
> >> target rdf pressure
> >> function
> 4*(eps1*eps2)**2*[((sig1+sig2)/2/x)**12-(sig1+sig2)/2/x)**6]
> > This should be square root and not Power 2.
> >
> > Christoph
> >> parameters eps1 sig1 eps2 sig2
> >>
> >>
> >> CG2-CG2
> >> target rdf presssure
> >> function  4*eps2*[(sig2/x)**12-(sig2/x)**6]
> >> parmeters eps2 sig2
> >>
> >> Thanks,
> >>
> >> --
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> >> "votca" group.
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> send
> >> an
> >> email to votca+un...@googlegroups.com.
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> >> For more options, visit https://groups.google.com/d/optout.
> >
> >
> >
> > --
> > Christoph Junghans
> > Web: http://www.compphys.de
> >>>
> >>> --
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> 

Re: [votca] energy group

[Sikandar Mashayak]

Hi Alireza,

Have you excluded interactions between bonded beads? One of your CG
molecule has 3 CG beads, so try excluding non-bonded interactions among
them and see if that works for you. You can use gromacs [exclusions]
setting in your topology to exclude the interactions.

Best,
Sikandar

On Tue, Feb 9, 2016 at 2:20 PM, Alireza Moradzadeh 
wrote:

> In fact, I did the same thing but it worked only for first step then it
> started to give me LINCS errors. Due to non equilibrated sys.
>
>
> > On Feb 9, 2016, at 12:24 PM, Christoph Junghans 
> wrote:
> >
> > 2016-02-08 17:40 GMT-07:00 Alireza Moradzadeh :
> >> Dear Christoph,
> >>
> >> Thank you for your email. But I encountered problem with implementation
> of it. I want to use PME as my coulomb type. So I have to put my three bead
> molecule beads in different charge groups. But I face severe problem with
> electrostatic interaction between beads which blows up my system. I am
> seeking a way to equilibrate this system.
> >
> > If you need to combine PME with tabulated interactions, you might need
> > to start from a different initial guess for the potentials, because
> > the Boltzmann inversion of the g(r) contains contributions from the
> > coulombic part, too.
> >
> > I would use a couple of pure LJ interactions for a start (put them as
> > NAME.pot.in in the same directory as settings.xml).
> >
> > Christoph
> >
> >> Thanks
> >> Alireza
> >>> On Feb 8, 2016, at 10:28 AM, Christoph Junghans 
> wrote:
> >>>
> >>> 2016-02-07 19:50 GMT-07:00 Alireza Moradzadeh :
>  Dear Users,
> 
>  Let's suppose I have two molecules one composed of three beads and the
>  second one composed of just one bead. mol1 : A B C & mol2 : D
>  what's is the number of energy groups in gromacs.  should it be
> like:  mol1
>  mol2  and energygrp_table: mol1 mol1 mol1 mol2 mol2 mol2 or A A A B A
> C A D
>  B B B C B D C C C D
> >>> Yes, that is correct!
> >>>
> 
>  Thanks,
>  Alireza
> 
>  --
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> >>>
> >>>
> >>>
> >>> --
> >>> Christoph Junghans
> >>> Web: http://www.compphys.de
> >>>
> >>> --
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> >>
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> >
> >
> > --
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> > Web: http://www.compphys.de
> >
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Re: [votca] Non-bonded interactions and electrostatic interaction

[Sikandar Mashayak]

Hi John,

Welcome to VOTCA user group.

I understand your coarse-graining problem as follows. You have a reference
atomic system containing your research molecule. Then you choose a mapping
scheme such that the coarse-grained beads in a CG molecule have charges on
them and now you want to determine a CG non-bonded interactions between
these CG beads.

So, in this case you can model your CG force field such that there are two
types of interactions between the CG beads: non-Coulombic short-range CG
potential + long-range Coulombic interactions. For the long-range Coulomb
forces you can use the methods such as PME and the non-Coulombic
short-range CG potential can be determined by one of the CG methods in
VOTCA. For example, assuming you are using GROMACS, to use the described CG
force field, the .mdp file options should be
.
.
.
coulombtype  = pme
vdw-type = User
.
.
.

and the rest you can follow from the tutorials.

I hope above suggestion helps.

Best,
Sikandar

On Wed, Dec 30, 2015 at 10:18 AM, John Voorehes  wrote:

> I am a new to the VOTCA package. I want to use this package for the
> coarse-graining simulation of my research molecule. Unlike the tutorial
> molecules, the beads for my molecule has charges. So, my question is, does
> the non-bonded interactions between two beads include Coulombic
> interactions too or is it just LJ potential/VDW? Are there any ways I can
> have coulombic interaction only?
>
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Re: [votca] Box volume for IBI runs

[Sikandar Mashayak]

Hi Pallavi,

In theory, if you keep the density same as the target system the volume for
NVT CG simulations for IBI would not affect. In practice, you should select
the size and length of the CG simulations large enough to obtain
statistically reliable RDF at each iteration. If your CG simulations are
too small you would face convergence issues.

So, you must keep the density of CG system same as target system and choose
size (volume) of the CG system large enough to obtain reliable RDFs.

I hope it clarifies.

Best,
Sikandar

On Wed, Dec 23, 2015 at 10:01 AM, Pallavi Banerjee <
pallavis...@students.iiserpune.ac.in> wrote:

> Hello all,
>
> Should the box volume to carry out NVT runs for IBI be the very same as
> that of the atomistic run? Would the difference in volume, if there was
> any, lead to issues in the convergence of the rdf profiles?
>
> Thanks in advance!
>
> -Pallavi Banerjee
>
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Re: [votca] Re: Box volume for IBI runs

[Sikandar Mashayak]

Hi Pallavi,

If you keep the density (N/V) the same, different sizes of the simulation
box for AA-MD and CG-MD won't make the difference. Here is why.

Assuming there are only one kind of CG particles in the system and we want
to reproduce the CG-CG RDFs. Then the RDF from the MD simulation can be
computed as

g(r) = Npair(r) / ( dV * (N/2) *(N/V) )

where, Npair(r) is the average number of pairs at distance 'r', dV is the
bin volume, N is the total number of CG particles, and V is the box volume.

As you can see from above definition, as long as you keep N/V the same,
difference in volumes won't matter. In other words, if you change volume
"V" you should also change "N" such that N/V is set to desired density.

Let us know if you have doubts about above clarification.

On Wed, Dec 23, 2015 at 11:18 AM, Pallavi Banerjee <
pallavis...@students.iiserpune.ac.in> wrote:

> Thank you for your reply, Sikandar. I am worried about the normalization
> of the rdf. Isn't that a volume normalization? If that is the case, I would
> think that different sizes of the simulation box for the atomistic and CG
> runs would make a difference. I might be wrong here, and hence need some
> clarification on this.
>
> Many thanks.
>
> -Pallavi Banerjee
>
>
> On Wednesday, December 23, 2015 at 10:31:24 PM UTC+5:30, Pallavi Banerjee
> wrote:
>>
>> Hello all,
>>
>> Should the box volume to carry out NVT runs for IBI be the very same as
>> that of the atomistic run? Would the difference in volume, if there was
>> any, lead to issues in the convergence of the rdf profiles?
>>
>> Thanks in advance!
>>
>> -Pallavi Banerjee
>>
>> --
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Re: [votca] Question about "a CG bead is chosen to be anywhere besides COM"

[Sikandar Mashayak]

Hi Nickya,

In VOTCA, there is no such restriction that CG bead must be at center of
mass. You can choose any site for the CG bead by specifying corresponding
mapping coefficients. You can find more info in the manual- see mapping
sections in chapter 2 and 3.

Best,
Sikandar

On Tue, Oct 20, 2015 at 12:31 AM,  wrote:

> Hello all,
>
> It is a default setting that a CG bead is chosen to be the center of mass
> of a group.
> I need a CG bead is chosen to be anywhere I want, but there is no guide
> about this in manual or tutorial.
> Can VOTCA implement this function?
>
> Thanks in advance,
> Nickya
>
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Re: [votca] Fmatch.xml query: single interactions vs all-at-once

[Sikandar Mashayak]

Hi Rom,

I do not think there is a restrictions on the number of interactions that
can be coarse-grained using force-matching.
Could you please give more details about the error which can be found in
inverse.log file.

Best,
Sikandar

On Tue, Oct 20, 2015 at 7:29 AM, Rom  wrote:

> Hi guys!
>
> I was force matching my intermolecular interactions, so had a big
> fmatch.xml with all my interactions and parameters (derived from csg_stat
> for each interaction). My query is then when I tried to generate potentials
> by using one large fmatch,xml file, it failed to run. Yet if I run each
> interaction separately from the fmatch.xml file, it is completely fine. Is
> there a correlation between each interaction in the fmatch.xml file? Is
> this something I should be concerned about, that the whole file fails to
> run, but each interaction is fine when i separate it?
>
> Apologies if this is a really obvious question lol
>
> Many thanks!
> Rom
>
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Re: [votca] meaning of removing all fmatch options in the example of SPC/E water

[Sikandar Mashayak]

Hi Changwoon Jang,

To obtain RDF from csg_stat, you need to provide only the non-bonded
interaction name, types, and grid dimension and spacings. In the case of
following is sufficient,


   
  

CG-CG
*
*

0.24
1.00
0.01
  



Similar settings are also needed for fmatch along with fmatch specific
stuff.  You can also use the fmatch.xml as an input to csg_stat and all
those settings between  ..  section will be ignored by
csg_stat.

I hope it clarifies some confusion.

Cheers,
Sikandar

On Mon, Oct 5, 2015 at 1:02 PM, Chang Woon Jang 
wrote:

> Dear VOTCA USER,
>
> I am following an example of SPC/E water. In the tutorial, it says
> "Copy the setting file fmatch.xml to dist.xml and remove all fmatch
> options from dist.xml. After this, calculate the center of mass RDF using 
> csg_stat".
>
>
> In the fmatch.xml, there are two fmatch options as follow. As you see,
> from line 3 to 6 from the top, and from 3 to 8 from the bottom.
>
> Do I need to remove all of these? I just removed the upper part (line 3 to
> 6 from the top), but it worked. I am a little bit confused about this.
>
> 
>   
>   
> false
> 5
>   
>   
>   
> 
> CG-CG
> *
> *
> 
> 0.24
> 1.00
> 0.01
> 
> 
>   0.24
>   1.00
>   0.02
>   0.002
> 
>   
> 
>
>
> Thank you very much for the clarification.
>
>
> Best regards,
> Changwoon Jang,
>
>
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Re: [votca] Error with csg_map

[Sikandar Mashayak]

Hi Changwoon Jang,

What was the version of the Gromacs library the VOTCA was linked to, when
it was built. I guess you upgraded your gromacs version, try rebuilding the
VOTCA with the latest gromacs.

Also, VOTCA 1.3 was recently released. Check it out at
https://github.com/votca/csg/releases

I hope it helps.

Best,
Sikandar

On Mon, Oct 5, 2015 at 8:57 AM, Chang Woon Jang 
wrote:

> Hi Votca User,
>
>I am trying to use csg_map and have the following error. Is there VOTCA
> version 5.0.6 to comparable with GROMACS 5.0.6?
>
> Thank you.
>
>  Reading file topol.tpr, VERSION 5.0.6 (single precision)
>
> ---
> Program VOTCA, VERSION 4.6.8-dev-20150706-eea54d0
> Source code file: /home/changwoon/VOTCA/src/gromacs/src/gmxlib/tpxio.c,
> line: 2978
>
> Fatal error:
> reading tpx file (topol.tpr) version 100 with version 83 program
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> ---
>
> "You Can Always Go On Ricky Lake" (Offspring)
>
>
> Best regards,
> Changwoon Jang,
>
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Re: [votca] Water csg_inverse tutorial

[Sikandar Mashayak]

Hi Marc,


With "cutoff-scheme = Group" gromacs should not give the same error again.

Did you clear the 'step_*' directories from the previous run and reran? It
may be the case than you only updated grompp.mdp in the main directory and
forgot to update the grompp.mdp in the step_001. Please check if that the
case.

If not please post the last few lines from inverse.log which describe above
error.

Thanks,
Sikandar

On Fri, Sep 18, 2015 at 10:34 AM, Marc Charendoff 
wrote:

> Hello,
>
> I tried the "cutoff-scheme = Group" insertion into the mdp file but it did
> not work. I got the very same errors as originally stated. Thoughts?
>
> Thanks, Marc
>
> --
> *From:* Christoph Junghans 
> *To:* "votca@googlegroups.com" 
> *Sent:* Thursday, September 17, 2015 5:04 PM
> *Subject:* Re: [votca] Water csg_inverse tutorial
>
> 2015-09-17 13:37 GMT-06:00 Marc Charendoff :
> > Moved on beyond the last posed question - figured out which options to
> > clear. Now attempting to run csg_inverse per the water tutorial  (using
> > lastest VOTCA and Gromacs 5.0.2):
> >
> > ERROR 1 [file grompp.mdp]:
> >  With Verlet lists only cut-off and PME LJ interactions are supported
> >
> > ERROR 2 [file grompp.mdp]:
> >  With Verlet lists only cut-off, reaction-field, PME and Ewald
> >  electrostatics are supported
> >
> > grompp.mdp file in the ibi directory of the tutorial for lists,
> > Electrostatics and VDW are as follows (I know there is a deprecation of
> > group-based cut-offs in 5.0, but per the error it  looks like Verlet is
> > being invoked which I'm not so sure it is) Is this a grompp.mdp error or
> > something with Votca?
> Yes. this is a gromacs problem! Even though group-based kernel have
> been deprecated, gromacs 5.0/5.1 does not support tabulated
> interactions, which are needed for VOTCA, in the new verlet cutoff
> scheme.
>
> As a workaround just add "cutoff-scheme = Group" to the mdp file.
> In votca-1.3-dev we do that trick automatically. The tutorial assumes
> that you have the dev version install, that is what the "d" in
> "./build.sh --prefix ${prefix} -ud ..." in Installation section stands
> for.
>
> Christoph
>
>
>
> >
> > ; NEIGHBORSEARCHING PARAMETERS
> > ; nblist update frequency
> > nstlist = 10
> > ; ns algorithm (simple or grid)
> > ns-type = Grid
> > ; Periodic boundary conditions: xyz, no, xy
> > pbc = xyz
> > periodic_molecules = no
> > ; nblist cut-off
> > rlist = 1
> > ; OPTIONS FOR ELECTROSTATICS AND VDW
> > ; Method for doing electrostatics
> > coulombtype = User
> > rcoulomb-switch = 0
> > rcoulomb = 0.9
> > ; Relative dielectric constant for the medium and the reaction field
> > epsilon_r = 1
> > epsilon_rf = 80
> > ; Method for doing Van der Waals
> > vdw-type = User
> > ; cut-off lengths
> > rvdw-switch = 0
> > rvdw = 0.9
> > ; Apply long range dispersion corrections for Energy and Pressure
> > DispCorr = EnerPres
> > ; Extension of the potential lookup tables beyond the cut-off
> > table-extension = 1
> > ; Seperate tables between energy group pairs
> > energygrp_table = CG CG
> > ; Spacing for the PME/PPPM FFT grid
> > fourierspacing = 0.12
> > ; FFT grid size, when a value is 0 fourierspacing will be used
> > fourier_nx = 0
> > fourier_ny = 0
> > fourier_nz = 0
> > ; EWALD/PME/PPPM parameters
> > pme_order = 4
> > ewald_rtol = 1e-05
> > ewald_geometry = 3d
> > epsilon_surface = 0
> > optimize_fft = no
>
> >
> >
> > --
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>
>
> --
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> Web: http://www.compphys.de
>
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Re: [votca] Input format not supported

[Sikandar Mashayak]

Hi Pallavi,

Could you please share inverse.log file? It has more detailed description
of the error.

Thanks,
Sikandar

On Thu, Sep 17, 2015 at 1:00 AM, Pallavi Banerjee <
pallavis...@students.iiserpune.ac.in> wrote:

> Hello users,
>
> This might strike you as a question too inane, but I am absolutely new to
> Votca.
>
> I am trying out the hexane tutorial. But the commands do not accept the
> gromacs created topology file. It says: input format not supported.
> I am using version 1.2.4 of votca compiled gromacs 4.6.7.  Is this a
> version incompatibility issue?
>
> Thanks and regards,
>
> Pallavi Banerjee.
>
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Re: [votca] Re: how to deal with 'undefined reference' while running ./build.sh

[Sikandar Mashayak]

Hi Chaofu Wu,

Try linking to shared libraries .so instead of static (.a). See if that
helps.

Best,
Sikandar

On Tue, Sep 15, 2015 at 7:58 AM, xiaowu759  wrote:

> Either of the following solutions posted previously can not deal with it
>
> install/build a shared version of fftw;
> specify a shared fftw to -DFFTW3_LIBRARY;
> add libm.so to -DFFTW3_LIBRARY
>
>
>
> --
> View this message in context:
> http://votca.966470.n3.nabble.com/how-to-deal-with-undefined-reference-while-running-build-sh-tp4024971p4024972.html
> Sent from the votca mailing list archive at Nabble.com.
>
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Re: [votca] Errors uuring building votca and gromacs using build.sh

[Sikandar Mashayak]

Hi Chang,

This sounds like you do not have write permission to the folder. In which
folder did you install tutorials? Make sure you have write permissions to
that folder.

Cheers,
Sikandar

On Wed, Aug 12, 2015 at 10:25 AM, Chang Woon Jang changwoonj...@gmail.com
wrote:

 Dear Sikandar Mashayak,


 Thank you very much for your advise. That is a great solution. I have
 another question.

 When I run ./run in csg-tutorials/propane/atomistic/ with superuser mode
 (su), it works. However, when I run the same thing without superuser, the
 following error occured.

 Is there any knowing solution? I very appreciate your help.


 ---
 Program grompp, VERSION 4.6.8-dev-20150706-eea54d0
 Source code file: /home/chang/VOTCA/src/gromacs/src/gmxlib/futil.c, line:
 542

 File input/output error:
 mdout.mdp
 For more information and tips for troubleshooting, please check the GROMACS
 website at http://www.gromacs.org/Documentation/Errors
 ---


 Best regards,
 Chang


 On Wed, Aug 12, 2015 at 12:03 PM, Sikandar Mashayak symasha...@gmail.com
 wrote:

 Hi Chang,

 The error says the cmake could not find GROMACS. Is gromacs installed on
 the machine? If yes, then make sure it is in the PATH.  Or you can also try
 building gromacs with  tools and csg by running

  ./build.sh --prefix ${prefix} -ud gromacs tools csg

 I hope it helps.

 Cheers,
 Sikandar

 On Wed, Aug 12, 2015 at 9:11 AM, CHANG changwoonj...@gmail.com wrote:

 Dear VOTCA users,

I followed the votca installation process. There is an error occured
 duing ./build.sh --prefix ${prefix} -ud tools csg


   1. su
 2. prefix=/home/chang/VOTCA
 3. mkdir -p ${prefix}/src
 4. cd ${prefix}/src
 5. wget http://votca.googlecode.com/hg/build.sh
 6. chmod +x build.sh
 7. ./build.sh --prefix ${prefix} -ud tools csg

 The following error ocuured. Would you please let me know what the
 problem is?
 Do I need to install gromacs first?



  -- Looking for sqrt in m - found
 -- checking for module 'libgmx_d'
 --   package 'libgmx_d' not found
 -- Could NOT find GROMACS (missing:  GROMACS_LIBRARY
 GROMACS_INCLUDE_DIR)
 -- checking for module 'libgmx'
 --   package 'libgmx' not found
 -- Could NOT find GROMACS (missing:  GROMACS_LIBRARY
 GROMACS_INCLUDE_DIR)
 -- checking for module 'libgromacs_d'
 --   package 'libgromacs_d' not found
 -- Could NOT find GROMACS (missing:  GROMACS_LIBRARY
 GROMACS_INCLUDE_DIR)
 -- checking for module 'libgromacs'
 --   package 'libgromacs' not found
 -- Could NOT find GROMACS (missing:  GROMACS_LIBRARY
 GROMACS_INCLUDE_DIR)
 CMake Error at src/libcsg/CMakeLists.txt:20 (message):
   gromacs not found, make sure you have installed at least the
 gromacs-4.0.7
   and it's dev package.  If the gromacs module was not found above, make
 sure
   you have sourced GMXRC or set PKG_CONFIG_PATH yourself.  (use option
   -DGROMACS_PKG_OVERWRITE=libgmx/_d for gromacs5.0 and
   -DGROMACS_PKG_OVERWRITE=libgromacs/_d for gromacs=5.0 to influence the
   search.


 -- Configuring incomplete, errors occurred!


 Thank you very much for your help.

 Best regards,
 Chang


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Re: [votca] problem in csg_inverse

[Sikandar Mashayak]

Hi Jin,

Did you check the inverse.log file? It may contain more information about
the error, if any.

--
Sikandar

On Tue, Jul 21, 2015 at 7:58 AM, jingyi.hu jingyi...@qmul.ac.uk wrote:

 Hi,

 I followed the ibi tutorial successfully before. However, when I used my
 own files to build ibi model, the program terminated without giving any
 error when I typed:

 *csg_inverse --debug --options settings.xml *

 The end of the debugging information shows as below:
 *...*
 *enable_logging*
 *+ local log*
 *+ [[ -z '' ]]*
 *++ csg_get_property cg.inverse.log_file*
 *Terminated*

 Can anybody help me with this problem?

 Regards

 Jin

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Re: [votca] how to get a CG trajectory with forces

[Sikandar Mashayak]

Hi Albert,

As Christoph suggested, it is not that hard to implement it. To get an idea
about how to read and write trajectories, you can look at traj_force
example in the csg application tools
https://code.google.com/p/votca/source/browse/?repo=csgapps#hg%2Ftraj_force.


I hope it helps.

Cheers,
Sikandar

On Tue, Apr 7, 2015 at 1:33 PM, Christoph Junghans jungh...@votca.org
wrote:

 Hi,

 Am 07.04.2015 07:52 schrieb Albert Solernou a.soler...@gmail.com:
 
  Hi,
  do you know how can I get a CG trajectory that includes the forces? I
 have  a gromacs trajectory and:
 Yes, this function is simply not implemented! It isn't hard to do, but
 nobody needed it so far.

 Cheers,

 Christoph

   csg_map --top md_1.tpr --trj md_1.trr --cg water.xml --out cg.trr
  outputs a cg trajectory that does not include the forces according to
   gmx check -f cg.trr
  although the velocites look correctly included when I add the --vel flag.
 
  Thanks,
  Albert
 
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Re: [votca] FIrst IBI iteration explodes

[Sikandar Mashayak]

Hi Dan,

As Denis correctly mentioned, IBI might not work for slab-like system in
which RDFs do not converge to 1. One other option, in addition to IBI-like
algorithm proposed in Denis's paper, is relative entropy minimization
method. We showed that it works for water confined in slab-like channels
http://link.aip.org/link/?JCPSA6/137/214707/1.

Best,
Sikandar

On Thu, Jan 29, 2015 at 6:55 AM, Denis Andrienko andrie...@googlemail.com
wrote:

 Hi Dan,

 If your RDF does not converge to 1 at large distances (e.g. if you do not
 have a bulk system) the IBI method might simply not work. Have a look at
 this paper:
 http://www2.mpip-mainz.mpg.de/~andrienk/publications/jochum_2012_a.pdf.
 You will see that for slab systems you can still use IBI-like alrorithm,
 but you will have to evaluate the 3-D RDF out of 2-D RDF.

 Best,
 Denis

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Re: [votca] RDF give different area under the curve after each iteration

[Sikandar Mashayak]

Hi Mohammad,

I think, area under the A-B RDF, (specifically \int g(r)4\pi r^2 dr) gives
you an estimate of total number of B type neighbours for A type particle,
which depends on the A-B interaction. During coarse-graining iterations,
A-B pair interaction is modified at each iteration (until convergence),
i.e., interaction may not be the same at different iteration steps, and
therefore, total number of neighbours and area under g(r) may vary at each
iteration step.

Regarding convergence, I also observed, due to statistical nature of short
CG-MD simulations at each iteration, CG pair potentials seem to oscillate
near convergence after few hundred iterations even though CG RDFs compare
well with the target RDFs. So, I suggest you try convergence criteria based
on the RDFs instead of potentials.

I hope that helps.

Best,
Sikandar

On Sun, Nov 30, 2014 at 10:57 PM, MSW mohd.alwaraw...@gmail.com wrote:

 Thanks Christoph for the reply!

 I run my system for 400 iterations and still my system did not converge at
 all. The value of the convergence decrease and then increase to some value,
 and after that it oscillate around a specific value. I only attached the
 first step as an example that the RDF area does not match.

 I thought that RDFs should give similar area! since my system does not
 change that much after each iteration, and VOTCA use the same normalization
 process. Whats interesting that the shape of the RDF after some iterations
 is similar, however, the value is a little bit different.

 You answered my question that the RDFs area should not be equal, however,
 I have to discuss this with my PI.

 Thanks again!

 On Sunday, November 30, 2014 6:48:45 PM UTC-6, Christoph Junghans wrote:

 2014-11-30 10:05 GMT-07:00 MSW mohd.al...@gmail.com:
  Dear VOTCA users,
 
  I am running a system composed of four types of beads in vacuum, and
 after
  each iteration I look at the RDF and compare between TGT and NEW
  distribution. I found out that the new RDF does not have the same area
 under
  the curve, however, they both have the same range for calculation.
 The areas under two arbitrary RDFs are not supposed to be the same, as
 RDF are not area-normalized, but normalized to go to 1 for r to
 infinity.

 
  The A-A.dist.tgt was calculated using VOTCA (csg_stat) from the
 atomistic
  data and A-A.dist.new was calculated inside the iteration from CG data.
 This
  important to look at since convergence in VOTCA is calculated based on
 the
  difference between the two RDFs.
 
  I attached the two RDFs and the current and new potentials (for 1st
 step)
  with this post.
 Not try to interpret too much in the difference between the RDFs after
 one iteration step.
 If it does not converge after hundreds of iterations, you should be
 worried.

 It is also important to note that the convergence is defined very
 differently through out the literature.
 VOTCA supports different measures incl. the l1 and l2 norm. The latter
 was using in the original VOTCA publication.

 
  I really appreciate your support.
 What is your question actually?

 
  Thanks
 
  Mohammad
 
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 Web: http://www.compphys.de

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Re: [votca] Relative-Entropy

[Sikandar Mashayak]

Hi Mohammad,

The extrapolated potential for r  rmin must be repulsive always, otherwise
CG-MD simulations will crash.

Both the linear and exponential extrapolations (given by following
expressions) use the slope of the potential at rmin from relative entropy
update.

'm = dy/dx
- constant:  ''\$y = y0\$''
- linear:  ''\$y = ax + b\\;\\;b = - m*x_0 + y_0\;\;a = m\$''
- exponential: ''\$y = a*exp(b*x)\\;\\;a = y0*exp(-m*x0/y0)\\;\\;b
= m/y_0\$''

However, exponential also uses the value of the potential at rmin. Hence,
at some relative entropy update, if the value of the potential at rmin
becomes negative, even though the slope is repulsive, then the extrapolated
potential may become attractive and the following CG-MD run may crash.
Therefore, the linear extrapolation is preferred.

Exponential extrapolation generally results in the more repulsive core than
the linear extrapolation. However, with careful choice of rmin based on the
target RDF, linear extrapolation also results in sufficiently repulsive
core. Hence, there may not  be much difference between the CG-MD
simulations with exponentially extrapolated potentials and that with the
linearly extrapolated potentials.

I hope above explanation answers your questions.

Cheers,
Sikandar

On Tue, Jul 15, 2014 at 7:06 PM, Hossein Motevaselian 
h.motevasel...@gmail.com wrote:

 Hi,

 I was looking at the relative entropy code and find out the current
 version only linearly extrapolates the knot values less than rmin.
 Is there any reason not to extrapolate exponentially? And does it make a
 difference?

 Sincerely,
 Mohammad

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Re: [votca] RE tutorial don't converge

[Sikandar Mashayak]

Hi Marc

Can you please send inverse.log file? It will have more details about the
failure.

Thanks
Sikandar


On Tue, May 6, 2014 at 5:40 PM, Marc Segovia marcsego...@gmail.com wrote:

 Hi Sikandar

 You are right the rdf are converged in spce/water.

  Now I move to other model, I fit settings.xml script, include as guess a
 initial value from ibi previous, but an old problem appears.

  table_average.sh: averaging with awk failed

 I saw in mailing list, this is an issue related with a mismatch in
 param.cur,  same happens in my case, steep-001 runs well, but in 002
 colapse, both files mismatch, different number of parameters.

 My develpement version is 1.88, from 19.10.2013, maybe this wasn't solved
 yet , so I need to update my dev version ?


 Thanking in advance by your help

 Best Regards
 Marc


 On Sat, May 3, 2014 at 1:29 PM, Sikandar Mashayak symasha...@gmail.comwrote:

 Hi Marc

 Did you check the CG-CG RDF at 300the step? How do they compare with the
 reference RDF?

 In my experience, I found that, in the case of bulk water, with the
 current RE minimization method in VOTCA,
 the CG potentials more or less converge to the values which reproduce
 target RDF in less than 200 iterations.
 However, due to statistical nature of short CG-MD simulations at every
 update step, the values of CG potentials
 fluctuate around the converged values. These fluctuations may or may not
 satisfy the convergence check criteria, i.e., they may be smaller or larger
 than the specified tolerance, and it depends on various setting parameters
 such as length of CG-MD simulations, relaxation parameters, and number of
 knot values.

 Therefore, it is always good to check the CG particle RDFs periodically
 to judge whether the RE minimization is
 converged or not. I guess, in VOTCA, there is a way to use CG particle
 RDFs as a measure to decide convergence. I will check how to do that and
 get back to you.

 We are also working on implementing alternative approach for RE
 minimization, which is a deterministic approach. It is based on reweighting
 strategy. You can read more about it in the article

 Chaimovich, Aviel, and M. Scott Shell. “Coarse-Graining Errors and
 Numerical Optimization Using a Relative Entropy Framework.” *The Journal
 of Chemical Physics* 134, no. 9 (March 3, 2011): 094112.
 doi:10.1063/1.3557038

 I hope it helps. Let us know if you have any further questions or
 suggestions.

 Thanks,
 Sikandar






 On Fri, May 2, 2014 at 4:31 PM, Marc Segovia marcsego...@gmail.comwrote:

 Hi

 Last days I run relative entropy tutorial, using votca 1.3, in spce
 water model
 After several days in my PC, finally the cg don't converge.

 step 300 done, needed 1083 secs
 Doing convergence check: default
 Iterations are not converged, going on

 My question is , this happens because a convergence of 0.001 is to
 small, or because numerical errors in my software or because the number of
 configuration to average is too low , 50 ? or something else.

 Thanking in advance by your help

 Best Regards

 Marc

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[votca] csg: Make error

[Sikandar Mashayak]

Hi

I am getting this error trying to build updated source code of csg.

src/libcsg/csgapplication.cc:120:45: error: ‘VisibleOptions’ was not
declared in this scope

I guess, the VisibleOptions() function is not yet defined in the votca
tools application or the changes to votca::tools are not yet pushed.

Any advice?

Thanks
Sikandar

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Re: [votca] Trying to run relative entropy tutorial

[Sikandar Mashayak]

Hi Marc

The advantage of Cubic B-splines functional form is that it is very
flexible and it can capture any shape provided that sufficiently large
number of knot values are used.

The knot values determine the grid-size for B-splines, i.e., dr =
Rcut/(nknots-3). Smaller the grid size more flexible
is the B-spline. But decreasing grid size, i.e. more knot values, increases
computational time of RE. So you
have to estimate the minimum number of knot values that will capture the CG
potential shape.

In the case of water, CG potential is known to have two-minima
core-softened shape. Hence to capture such a
shape we used 48 knot values to model B-Splines. Since, we use cut-off of
0.9 nm, the grid size for B-spline is 0.02 nm (cut-off/(nknots-3)).

I hope this helps.

Regards
Sikandar


On Mon, Apr 14, 2014 at 12:50 PM, Marc Segovia marcsego...@gmail.comwrote:

 Hi all

  I am running RE tutorial in develpment version, but a question arise.
  When is estimated  the potential using  cubic splines, how do you
 specifed  the number of knots ? in the tutorial they are 48.

 !-- function form for the potential (lj126 or ljg or cbspl)--
   functioncbspl/function
   cbspl
 !-- no. of knots for cbspl function --
 nknots48/nknots

  Thanking in advance your help

  Best Regards

  Marc

  Dr. Marc Segovia
  CCBG-DETEMA
  Facultad de Quimica
  Universidad de la Republica
  11800 Montevideo
  Uruguay



 On Fri, Nov 1, 2013 at 11:57 PM, Sikandar Mashayak 
 symasha...@gmail.comwrote:

 Hi Marc

 The option nknots_cutoff was earlier used in the settings.xml file to
 specify number of cubic B-spline knots near the cut off which should be
 forced to value 0.0 to ensure that CG potential smoothly goes to zero near
 the cut-off.

 Later, I decided  to fix this nknots_cutoff = 4 because I think fixing 4
 knot values near the cut-off is sufficient in most of the cases and user
 should not worry about this number. Hence, instead of taking this number as
 an input from user, it is fixed in the source code.

 You should not get the error property not found: nknots_cutoff if you
 are using latest source code of votca-csg (i.e., revision  
 681d33b7942bhttp://code.google.com/p/votca/source/detail?r=681d33b7942bba2d3d213f4e321b17e0c6a00676repo=csg).


 So could you please check if you are correctly downloading the latest
 version and installing it. Because, I dont get the same error, when I test
 the water spce relative entropy tutorial with the latest development
 version of csg source code.

 You can check if you are using the latest version of votca-csg by running
 csg_inverse -h it will print out the version of votca-csg that you are
 using.

 Let us know if you face issues with updating and installing the latest
 development version of votca-csg.

 Thanks
 Sikandar



 On Fri, Nov 1, 2013 at 6:03 PM, Marc Segovia marcsego...@gmail.comwrote:

 Good Night Everyone

 I am trying to run re tutorial with spce, but an error appear about
 nknots_cutoff property, I update my dev version without sucess, any
 suggestion ?

 Wishing a very good weekend and thanking in advance .

 Marc

 Dr. Marc Segovia
 CCBG
 Facultad de Quimica
 Universidad de la Republica
 11800 Montevideo
 Uruguay

 ~/votca1.3/csg-tutorials.votca-695b567ead5c/spce/re/step_000
 Generating potential tables from the initial parameters
 Running critical command 'csg_reupdate --gentable true --param-in-ext
 param.new --options
 /home/marc/votca1.3/csg-tutorials.votca-695b567ead5c/spce/re/settings.xml'
 an error occurred:
 property not found: nknots_cutoff

 Callstack:
 /home/marc/votca1.3/share/votca/scripts/inverse/inverse.sh - linenumber
 166
 do_external - linenumber 171 in
 /home/marc/votca1.3/share/votca/scripts/inverse/functions_common.sh
 /home/marc/votca1.3/share/votca/scripts/inverse/prepare_re.sh -
 linenumber 36
 critical - linenumber 4 (see 'csg_call --cat function
 critical')
 die - linenumber 2 (see 'csg_call --cat function die')

 
 #
 #
 #
 ERROR:
 #
 # critical: 'csg_reupdate --gentable true --param-in-ext param.new
 --options
 /home/marc/votca1.3/csg-tutorials.votca-695b567ead5c/spce/re/settings.xml'
 failed #
 # For details see the logfile
 /home/marc/votca1.3/csg-tutorials.votca-695b567ead5c/spce/re/inverse.log
 #
 #
 #

 
 die: (called from 318)  CSG_MASTER_PID is 31799
 die: pids to kill: 31799 318

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Re: [votca] Re: Installing VOTCA on a cluster

[Sikandar Mashayak]

Hi Hossein

Christoph figured out that the segfault issue, in the above case, occurred
because of wrong GROMACS precision specification
while building csg.

By default, the csg was built assuming double precision for GROMACS though
the precision of an installed GROMACS was single.

The precision of GROMACS library while building csg could be set by the
cmake option of -DGROMACS_DEFINITIONS= (i) blank (nothing) for single and
(ii) -DGMX_DOUBLE for double.

The default value was -DGROMACS_DEFINITIONS=-DGMX_DOUBLE, and the gromacs
that ./build.sh installed was a single precision.
And hence, you get a segmentation fault!

This issue is fixed by Christoph. Now cmake tries to guess the precision
from the actual installed GROMACS library, instead of
assuming it to be double.

So pull the changes and check if it works. If you want to be certain,
manually specify the option -DGROMACS_DEFINITIONS
when you build csg.

I hope it helps.

Cheers
Sikandar




On Sun, Feb 16, 2014 at 2:04 AM, Sikandar Mashayak symasha...@gmail.comwrote:

 Hi Christoph

 Segfault is occurring due to, in my particular case, bead-getResnr() is
 greater than the top.ResidueCount().

 I checked topology using gmxdump, it looks fine to me. I am, however, not
 yet sure why is there inconsistency
 in the resdue counts.

 I have attached the input files for csg_stat, can you please check if you
 also get the segfault?

 Thanks
 Sikandar



 On Fri, Feb 14, 2014 at 9:21 PM, Christoph Junghans jungh...@votca.orgwrote:

 2014-02-14 12:59 GMT-07:00 Sikandar Mashayak symasha...@gmail.com:
  Hi Christoph
 
  The output of the gdb backtrace is:
 
  #0  std::operator char, std::char_traitschar, std::allocatorchar
 
  (__os=..., __str=
  Traceback (most recent call last):
File
 
 /usr/local/gcc-4.7.1/lib64/../share/gcc-4.7.1/python/libstdcxx/v6/printers.py,
  line 602, in to_string
  header = ptr.cast(reptype) - 1
  RuntimeError: Cannot access memory at address 0x39
  ) at
 
 /usr/local/gcc-4.7.1/build/x86_64-unknown-linux-gnu/libstdc++-v3/include/bits/basic_string.h:2755
  #1  0x77b81335 in votca::csg::GMXTopologyReader::ReadTopology
  (this=0x68ddb0, file=topol_nowf.tpr, top=...)
  at
 
 /home/mashaya1/Apps/votca/src/csg/src/libcsg/modules/io/gmxtopologyreader.cc:145
 This line 145 has been there for a long time, but my guess is that
 something goes wrong with the residue numbers:
 top.getResidue(res_offset + bead-getResnr())-getName()

 Can you check with gmdump, if the Residue numbers in your tpr start
 with 0 and are contiguous.

 Christoph

  #2  0x77b47377 in votca::csg::CsgApplication::Run
  (this=0x7fffcbe0)
  at
 /home/mashaya1/Apps/votca/src/csg/src/libcsg/csgapplication.cc:215
  #3  0x77844fbc in votca::tools::Application::Exec(int, char**)
 ()
 from /home/mashaya1/Apps/votca/lib/libvotca_tools.so.3
  #4  0x0044fca8 in main (argc=7, argv=0x7fffd078)
  at /home/mashaya1/Apps/votca/src/csg/src/tools/csg_stat.cc:116
 
  ---
  Sikandar
 
 
  On Thu, Feb 13, 2014 at 10:10 PM, Hossein Motevaselian
  h.motevasel...@gmail.com wrote:
 
  Thank you Christoph,
  I finally installed it without any errors, but as Sikandar said I am
  getting this segment fault error while using the votca commands.
  I will follow your discussions.
  Thanks again
 
  On Thursday, February 13, 2014 3:47:54 PM UTC-6, Christoph Junghans
 wrote:
 
  2014-02-13 14:34 GMT-07:00 Sikandar Mashayak symas...@gmail.com:
   Hi
  
   On the same cluster (as Hossein), I was able to successfully install
   votca-tools and csg with the cmake option:
  
   -DBoost_INCLUDE_DIR=/usr/local/boost/boost-1.51.0/include/
  
   Though, the installation is complete. I get the segmentation faults
   when I
   run any csg application, e.g., csg_stat .
  
   I am guessing this is related to boost. Am I right? I am not sure
 how
   to
   trace the cause of the segmentation fault.
  Build with -DCMAKE_BUILD_TYPE=Debug and then run:
  $ gdb --args csg_stat options...
  in gdb type run, it will run until the segault and then type bt
  (backtrace).
 
  Cheers,
 
  Christoph
 
  
   Thanks
   Sikandar
  
  
   On Thu, Feb 13, 2014 at 8:27 PM, Denis Andrienko
   andr...@googlemail.com
   wrote:
  
   You might also need to specify
  
  
 -DBoost_FILESYSTEM_LIBRARY=/usr/local/boost/boost-1.51.0/lib/libboost_filesystem.so
  
  
   As I have already mentioned, boost has several bugs in major
 releases.
   We
   haven't tested 1.51, but I had to downgrade it in the latest UBUNTU
   release.
   We know that 1.49 and 1.54 are working. Also make sure that you
 don't
   have
   several versions installed at the same time:
  
  
   dpkg -s libboost-dev | grep 'Version'
   or
   cat /usr/include/boost/version.hpp | grep BOOST_LIB_VERSION
  
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Re: [votca] Re: Installing VOTCA on a cluster

[Sikandar Mashayak]

Hi Christoph

The output of the gdb backtrace is:

#0  std::operator char, std::char_traitschar, std::allocatorchar 
(__os=..., __str=
Traceback (most recent call last):
  File
/usr/local/gcc-4.7.1/lib64/../share/gcc-4.7.1/python/libstdcxx/v6/printers.py,
line 602, in to_string
header = ptr.cast(reptype) - 1
RuntimeError: Cannot access memory at address 0x39
) at
/usr/local/gcc-4.7.1/build/x86_64-unknown-linux-gnu/libstdc++-v3/include/bits/basic_string.h:2755
#1  0x77b81335 in votca::csg::GMXTopologyReader::ReadTopology
(this=0x68ddb0, file=topol_nowf.tpr, top=...)
at
/home/mashaya1/Apps/votca/src/csg/src/libcsg/modules/io/gmxtopologyreader.cc:145
#2  0x77b47377 in votca::csg::CsgApplication::Run
(this=0x7fffcbe0)
at /home/mashaya1/Apps/votca/src/csg/src/libcsg/csgapplication.cc:215
#3  0x77844fbc in votca::tools::Application::Exec(int, char**) ()
   from /home/mashaya1/Apps/votca/lib/libvotca_tools.so.3
#4  0x0044fca8 in main (argc=7, argv=0x7fffd078)
at /home/mashaya1/Apps/votca/src/csg/src/tools/csg_stat.cc:116

---
Sikandar


On Thu, Feb 13, 2014 at 10:10 PM, Hossein Motevaselian 
h.motevasel...@gmail.com wrote:

 Thank you Christoph,
 I finally installed it without any errors, but as Sikandar said I am
 getting this segment fault error while using the votca commands.
 I will follow your discussions.
 Thanks again

 On Thursday, February 13, 2014 3:47:54 PM UTC-6, Christoph Junghans wrote:

 2014-02-13 14:34 GMT-07:00 Sikandar Mashayak symas...@gmail.com:
  Hi
 
  On the same cluster (as Hossein), I was able to successfully install
  votca-tools and csg with the cmake option:
 
  -DBoost_INCLUDE_DIR=/usr/local/boost/boost-1.51.0/include/
 
  Though, the installation is complete. I get the segmentation faults
 when I
  run any csg application, e.g., csg_stat .
 
  I am guessing this is related to boost. Am I right? I am not sure how
 to
  trace the cause of the segmentation fault.
 Build with -DCMAKE_BUILD_TYPE=Debug and then run:
 $ gdb --args csg_stat options...
 in gdb type run, it will run until the segault and then type bt
 (backtrace).

 Cheers,

 Christoph

 
  Thanks
  Sikandar
 
 
  On Thu, Feb 13, 2014 at 8:27 PM, Denis Andrienko 
 andr...@googlemail.com
  wrote:
 
  You might also need to specify
  -DBoost_FILESYSTEM_LIBRARY=/usr/local/boost/boost-1.51.0/lib/libboost_filesystem.so

 
 
  As I have already mentioned, boost has several bugs in major releases.
 We
  haven't tested 1.51, but I had to downgrade it in the latest UBUNTU
 release.
  We know that 1.49 and 1.54 are working. Also make sure that you don't
 have
  several versions installed at the same time:
 
 
  dpkg -s libboost-dev | grep 'Version'
  or
  cat /usr/include/boost/version.hpp | grep BOOST_LIB_VERSION
 
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 --
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 Web: http://www.compphys.de

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Re: [votca] Re: Installing VOTCA on a cluster

[Sikandar Mashayak]

Hi

On the same cluster (as Hossein), I was able to successfully install
votca-tools and csg with the cmake option:

-DBoost_INCLUDE_DIR=/usr/local/boost/boost-1.51.0/include/

Though, the installation is complete. I get the segmentation faults when I
run any csg application, e.g., csg_stat .

I am guessing this is related to boost. Am I right? I am not sure how to
trace the cause of the segmentation fault.

Thanks
Sikandar


On Thu, Feb 13, 2014 at 8:27 PM, Denis Andrienko
andrie...@googlemail.comwrote:

 You might also need to specify 
 -DBoost_FILESYSTEM_LIBRARY=/usr/local/boost/boost-1.51.0/lib/libboost_filesystem.so


 As I have already mentioned, boost has several bugs in major releases. We 
 haven't tested 1.51, but I had to downgrade it in the latest UBUNTU release. 
 We know that 1.49 and 1.54 are working. Also make sure that you don't have 
 several versions installed at the same time:

 dpkg -s libboost-dev | grep 'Version'
 or
 cat /usr/include/boost/version.hpp | grep BOOST_LIB_VERSION

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Re: [votca] Re: No convergence file found

[Sikandar Mashayak]

Hi Chaofu Wu

Where did you add
post_addconvergence/post_add ?

It should be specified for at least one interaction like below

cg
  bonded
...
...
inverse
 
 
 post_addconvergence/post_add
...
   /inverse
  /bonded

...
/cg

I hope this helps.

---
Sikandar




On Fri, Jan 3, 2014 at 1:45 PM, xiaowu759 xiaowu...@gmail.com wrote:

 Dear Chandan,
 Thank you very much for your reply. I added the lines according to your
 suggestion, but the errors remain unchanged. I wish to get further help.
 Best regards,
 Chaofu Wu



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Re: [votca] csg_map says output format not supported

[Sikandar Mashayak]

Hi Sergey

Even I had tried installing VOTCA on Windows using Cygwin, and faced the
similar issues of linking to gromacs libraries. I haven't yet figured out
the way to resolve it. If you figure it out, please let me know.

Thanks
Sikandar


On Wed, Dec 11, 2013 at 5:47 AM, Sergey Larin svlari...@gmail.com wrote:

 Hi, Christoph!

 среда, 11 декабря 2013 г., 4:54:06 UTC+4 пользователь Christoph Junghans
 написал:

 2013/12/10 Sergey Larin svla...@gmail.com:
  Hello, everyone!
 
  I'm trying to start using VOTCA a polymer simulated in my group. First,
 I've
  installed it and it seems to work. Then, I've created a mapping file
 and
  ready to start with VOTCA itself.
 
  I tried to run csg_map for my simple system with a command taken from
 the
  VOTCA manual:
  csg_map.exe --top topol.tpr --trj traj.xtc --cg O-BAPB_8.xml --out
  csg_out.gro
 
  The output of this command is the following
  Reading file topol.tpr, VERSION 4.6.3 (single precision)
  I have 570 beads in 1 molecules
  I have 88 beads in 1 molecules for the coarsegraining
  Reading frame   0 time0.000
  writing coarse-grained trajectory to csg_out.gro
  an error occurred:
  output format not supported: csg_out.gro
 Uh, is this Windows? If so, Windows is not supported or at least
 completely untested.


 Yes, it is Windows 7 64-bit and cygwin. It seems that there is some
 problems due to incompatibility in the dynamic loading libraries mechanism.
 Anyway, I've installed VOTCA on my second OS (fortunately, it's Linux).
 Everything works fine there. Now, I'm trying to understand what I have to
 do after mapping to obtain all potentials required to start CG simulations.
 Hope it will not take a long time.

 Sincerely,
 Sergey

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Re: [votca] convert csg potential to tab

[Sikandar Mashayak]

You are welcome Zhicheng.

Chandan, please pull the latest changes in votca.csg, Christoph has
corrected the issue in csg_call.

---
Sikandar


On Wed, Nov 13, 2013 at 12:00 AM, 郭志成 zcguo1...@gmail.com wrote:

 Hi  Sikandar:
 You are right. I made some mistakes about the parameters for potential
 conversion to espresso potential tables.
  It is working now based on youre suggestion. Thank you very much!
 Best Wishes!
 Zhicheng


 2013/11/13 Sikandar Mashayak symasha...@gmail.com

 Hi

 I am sorry I was not clear in my response.

 The reason for the errors was that the table.xml file provided by you did
 not contain all the required parameters for potential conversions to
 espresso potential tables. Also, the sequence of parameters inside the
 table.xml file was not right.

 I have corrected the table.xml file, which is attached below.  May be you
 can compare it with earlier settings to understand what was going wrong.

 I hope this helps.

 Cheers
 Sikandar


 On Thu, Nov 7, 2013 at 3:14 AM, 郭志成 zcguo1...@gmail.com wrote:

 Hi

 Thanks for your suggestion. For your comment, however, it is the method
 of calculating the coarse-grained potential using ibi procedure by espresso
 soft. I have obtained the coarse-grained potential (CG-CG.pot) calculated
 by gromacs with ibi procedure. I want to convert this potential to espresso
 format using csg_call convert_potential espresso. Anyway, thanks again for
 your reply.

 2013/11/7 Chandan Choudhury iitd...@gmail.com


  On Wed, Nov 6, 2013 at 9:32 PM, Sikandar Mashayak 
 symasha...@gmail.com wrote:

Hi

 I am trying to reproduce the error, but when I run the same command
 'csg_call --options table.xml --ia-type non-bonded --ia-name
 CG-CG convert_potential espresso CG-CG.pot tab', the command just get 
 stuck
 and I am not getting any error or any kind of output.

 I am not sure why is csg_call getting stuck.


 Hi Sikandar,

 I second your observation.
 This behavior is true for the 1.3-dev version. But if I try it on 1.2.3
 it executes. As I need to toggle between the two versions, this was never a
 problem for for me.

  Chandan


 Anyway, I guess, issue of property 'max' not found is due to
 incomplete information in table.xml. Try using the settings.xml given in
 ibi_esspresso tutorial instead of your table.xml. I hope that should work
 well.

 --
 Sikandar


 On Wed, Nov 6, 2013 at 2:46 AM, Zhicheng zcguo1...@gmail.com wrote:

  Hi Christoph:

 Thanks for your reply. I use the 'csg_call --options table.xml
 --ia-type non-bonded --ia-name CG-CG convert_potential espresso CG-CG.pot
 tab' to convert the coarse-grained potential(CG-CG.pot) calculated by
 gromacs ibi procedure to espresso format(tab). However, I get the 
 following
 error message:


 csg_get_interaction_property: Could not get 'max' for interaction with 
 name 'CG-CG'
 from table.xml and no default was found in


 /home/adminuser/votca_ctp/share/votca/xml/csg_defaults.xml Details can 
 be found above .


 在 2013年11月6日星期三UTC+8上午12时47分44秒，Christoph Junghans写道：

 2013/11/5 郭志成 zcgu...@gmail.com:
  Hi:
 
  I convert the csg potential files to the tab format (as read by
 espresso)
  using table_to_tab.pl (csg_call convert_potential tab).
 
  However, it needed three parameters (table_to_tab.sh in_pot
 in_deriv_pot
  outfile).
 
  The problem is that I can not understand the meaning of
 in_deriv_pot. How
  can I obtain the in_deriv_pot?
 csg_call convert_potential tab is just the low level script, which
 need an extra  file with the derivatives in it.

 csg_call convert_potential espresso
 should do what you want to do.

 
  I will be very appreciable for any suggestion.
 
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Re: [votca] Trying to run relative entropy tutorial

[Sikandar Mashayak]

Hi Marc

The option nknots_cutoff was earlier used in the settings.xml file to
specify number of cubic B-spline knots near the cut off which should be
forced to value 0.0 to ensure that CG potential smoothly goes to zero near
the cut-off.

Later, I decided  to fix this nknots_cutoff = 4 because I think fixing 4
knot values near the cut-off is sufficient in most of the cases and user
should not worry about this number. Hence, instead of taking this number as
an input from user, it is fixed in the source code.

You should not get the error property not found: nknots_cutoff if you are
using latest source code of votca-csg (i.e., revision 
681d33b7942bhttp://code.google.com/p/votca/source/detail?r=681d33b7942bba2d3d213f4e321b17e0c6a00676repo=csg).


So could you please check if you are correctly downloading the latest
version and installing it. Because, I dont get the same error, when I test
the water spce relative entropy tutorial with the latest development
version of csg source code.

You can check if you are using the latest version of votca-csg by running
csg_inverse -h it will print out the version of votca-csg that you are
using.

Let us know if you face issues with updating and installing the latest
development version of votca-csg.

Thanks
Sikandar



On Fri, Nov 1, 2013 at 6:03 PM, Marc Segovia marcsego...@gmail.com wrote:

 Good Night Everyone

 I am trying to run re tutorial with spce, but an error appear about
 nknots_cutoff property, I update my dev version without sucess, any
 suggestion ?

 Wishing a very good weekend and thanking in advance .

 Marc

 Dr. Marc Segovia
 CCBG
 Facultad de Quimica
 Universidad de la Republica
 11800 Montevideo
 Uruguay

 ~/votca1.3/csg-tutorials.votca-695b567ead5c/spce/re/step_000
 Generating potential tables from the initial parameters
 Running critical command 'csg_reupdate --gentable true --param-in-ext
 param.new --options
 /home/marc/votca1.3/csg-tutorials.votca-695b567ead5c/spce/re/settings.xml'
 an error occurred:
 property not found: nknots_cutoff

 Callstack:
 /home/marc/votca1.3/share/votca/scripts/inverse/inverse.sh - linenumber 166
 do_external - linenumber 171 in
 /home/marc/votca1.3/share/votca/scripts/inverse/functions_common.sh
 /home/marc/votca1.3/share/votca/scripts/inverse/prepare_re.sh -
 linenumber 36
 critical - linenumber 4 (see 'csg_call --cat function
 critical')
 die - linenumber 2 (see 'csg_call --cat function die')

 
 #
 #
 #
 ERROR:
 #
 # critical: 'csg_reupdate --gentable true --param-in-ext param.new
 --options
 /home/marc/votca1.3/csg-tutorials.votca-695b567ead5c/spce/re/settings.xml'
 failed #
 # For details see the logfile
 /home/marc/votca1.3/csg-tutorials.votca-695b567ead5c/spce/re/inverse.log
 #
 #
 #

 
 die: (called from 318)  CSG_MASTER_PID is 31799
 die: pids to kill: 31799 318

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Re: [votca] Re: averaging from awk failed

[Sikandar Mashayak]

Thanks Christoph

You are right! There was an issue with writing out updated parameters for
b-spline potentials.
I have corrected it. Soon, before the workshop, I will merge the changes
with default.

Cheers
Sikandar


On Mon, Sep 30, 2013 at 3:21 PM, Christoph Junghans jungh...@votca.orgwrote:

 Hi Sikandar,

 I found it, there was a typo in awk script, so the error message got
 lost, but the error was valid.
 The x values of the two param files mismatch and hence
 table_average.sh, gives an error.

 Cheers,

 Christoph

 2013/9/30 Sikandar Mashayak symasha...@gmail.com:
  Hi Christoph
 
  Please find attached the step_001/CG-CG.param.cur and
  step_002/CG-CG.param.cur.
 
  Thanks
  Sikandar
 
 
  On Mon, Sep 30, 2013 at 10:42 AM, Sikandar Mashayak 
 symasha...@gmail.com
  wrote:
 
  Hi
 
  I am trying to make sure SPC/E water relative entropy tutorial works
 well
  after I made few modifications to csg code.
 
  However, I am getting the table averaging error:
 
  table_average.sh: averaging with awk failed
 
  The log file is attached.
 
  Not sure why this error occurring in step_002 while averaging seems to
  have worked well for step_001.
 
  I guess, once this is issue is resolved, it should be ok to merge
  'sikandar' branch to 'default'.
 
  Thanks
  Sikandar
 
 
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[votca] Re: averaging from awk failed

[Sikandar Mashayak]

Hi Christoph

Please find attached the step_001/CG-CG.param.cur and
step_002/CG-CG.param.cur.

Thanks
Sikandar


On Mon, Sep 30, 2013 at 10:42 AM, Sikandar Mashayak symasha...@gmail.comwrote:

 Hi

 I am trying to make sure SPC/E water relative entropy tutorial works well
 after I made few modifications to csg code.

 However, I am getting the table averaging error:

 table_average.sh: averaging with awk failed

 The log file is attached.

 Not sure why this error occurring in step_002 while averaging seems to
 have worked well for step_001.

 I guess, once this is issue is resolved, it should be ok to merge
 'sikandar' branch to 'default'.

 Thanks
 Sikandar


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CG-CG.param.cur
Description: Binary data


CG-CG.param.cur
Description: Binary data

Re: [votca] IBI - decreasing potential minima with iterations

[Sikandar Mashayak]

Hi

I am just jumping in the discussion. So far what I follow is that there are
two main concerns in the case of heterogeneous systems IBI. First is that
RDF may not go to 1.0 near the cut-off and second is shifting of potentials
by VOTCA. So I am thinking can we try following to address these two issues

1. Can one use g_rdf s -fade like option to smoothly transform rdf to 1
beyond cut-off? Or will that be unphysical?

2. Can one use Splines to model IBI CG potentials and force knot values
near cut-off to be zero to smoothly take potentials to zero without
shifting?




thanks
Sikandar


On Fri, Jul 19, 2013 at 7:04 AM, s.neuman...@gmail.com wrote:

 Thank you for this.
 I recalculated my distributions and make them a value between 0 and 1 at
 large distances. If I submit then my own potential pot.in which goes to a
 positive value in this case would votca not shift the potential after each
 iteration to zero? Please, let me know.

 Steven

 W dniu środa, 17 lipca 2013 17:43:51 UTC+1 użytkownik Christoph Junghans
 napisał:

 2013/7/17  s.neu...@gmail.com:
  Thank you for this.
 
  Another question - presumably I will specify my own distributions (not
 from
  VOTCA) with some simplifications. Then I will create intial potentials
 to
  IBI as name.pot.in. Votca will try to fit to my distributions to the
 one
  submitted in the main directory. However, by calculating distributions
 after
  each step these will not be distributions which could possibly match my
  initial with simpifications, am I right? Do I have to calculate RDFs at
 each
  step on my own then?
 1.) If you give VOTCA a pot.in, it will not do use the potential of
 mean as initial guess in step_000, but just your potential.
 2.) Independently of pot.in, VOTCA will always compare dist.new
 against dist.tgt every step
 3.) dist.new is calculated in every iteration using csg_stat, you
 could make VOTCA fit only the part 0 to min.
 3b.) You could write a custom post-update script to do whatever rdf
 calculation/ potential modification after you want. This can be used
 to overwrite rdf calculated by csg_stat.
 3c.) All of this seems a bit hacky, why don't you just declare some
 interaction of type bonded, so csg_stat will calculate
 p(r)=H(r)/(4pi*r^2) instead of the rdf for those.

  Another issue: How Votca normalize RDFs using csg_stat ? I wish to have
  volume and mass normalized distributions, is that possible?
 No, we don't have an option to calculate the  volume and mass
 normalized distributions instead. Though it is not hard to implement!
 For IBI that would also make no difference as all normalization
 factors drop out in the ratio g(r)/g_target(r) used in the update.

 Christoph


 
  Steven
 
  W dniu wtorek, 16 lipca 2013 23:17:05 UTC+1 użytkownik Christoph
 Junghans
  napisał:
 
  2013/7/16  s.neu...@gmail.com:
  
  
   W dniu wtorek, 16 lipca 2013 08:48:51 UTC+1 użytkownik Tristan
 Bereau
   napisał:
  
   That sounds like what I was hinting at: from what I understand,
 you're
   simulating a single protein, not a pure liquid of stuff. So your
 RDF
   will never go to 1 because there won't be anything at large
 distances.
   Is that the case? If so, more iterations and/or better initial
 guesses
   won't cut it.
  
  
   Yes, this is the case. I will aproximate the RDFs so that they go to
 sth
   which is non zero. Thank you.
  non zero will not be enough, it has to be 1 otherwise your potential
  will still accumulated whatever the value, kT*log(P(r_cut), at the
  cutoff is.
 
  For me the distributions looks more like a something, which could be
  modeled with a non-linear spring type potential (r- +/-inf P-inf),
  where the minimum is a zero.
  VOTCA could do that for you if declare the interaction as bonded.
  (VOTCA's definition of non-bonded and bonded might not be taken too
  strict.)
  Also from the modeling point of view, it might make sense to have a
  spring between some beads, which cannot go infinitely apart due to
  geometry.
 
  Anyhow, these are scientific decisions you have to make yourself.
 
  Christoph
 
  
   Steven
  
  
   On Mon, Jul 15, 2013 at 10:09 PM,  s.neu...@gmail.com wrote:
Thank you for this. For heterogenous system RDF does not go to 1
 but
to
0.
In this case I guess I need thousands of iterations... The system
input
are
15 potentials which makes it so complicated.
   
Steven
   
W dniu poniedziałek, 15 lipca 2013 17:44:46 UTC+1 użytkownik
Christoph
Junghans napisał:
   
2013/7/15  s.neu...@gmail.com:
 Votca is definitely wrong. If you take the example of maximum
 of
 my
 ACI-ACI.dist.tgt the maximum corresponds to 65.555. The
 potential
 at
 this
 point should be: W = -2.49435*ln(65.55) = -10.433 and in my
 ACI-ACI.dist.pot
 the value corresponds to -16.1 - it is a huge difference and
 that
 is
 why
 my
 further distributions are so huge
No, Votca is 100% correct, and does what it is supposed to 

Re: [votca] mapping file for mixtures

[Sikandar Mashayak]

Hi Hossein

As Victor said, you have to create individual mapping file for each
molecule. Also, note that when you use csg_map with --trj traj.trr option,
by default, all the frames in traj.trr will be mapped and written to ouput
file, i.e., --out cg.gro, resulting in very large gro file containing
mapped CG coordinates of each frame in traj.trr. However, if your objective
is just to create initial CG .gro file for coarse-graining, such as by IBI,
I would suggest you use options --nframes 1 --begin teq so that csg_map
would map only single frame from traj.trr at time teq, where teq is the
time in ps at which it is safe to assume AA-MD trajectories are
equilibrated.

Good luck
Sikandar


On Tue, May 21, 2013 at 6:10 AM, Victor Ruehle rue...@votca.org wrote:

 Dear Hossein,

 multiple molecules per xml is currfently not supported. Instead, put them
 in separate xml files an specify both files when calling csg_map, i.e.:
 csg_map --cg mol1.xml;mol2.xml 

 Cheers,
 Victor




 2013/5/21 Hossein Motevaselian h.motevasel...@gmail.com

 Hi

 I am trying to prepare a mapping file for a mixture with two distinct
 molecules. However, when I use the command csg_map --top topol.tpr --trj
 traj.trr --cg  mixture.xml --out cg.gro,
 only the molecule that comes first in the mixture.xml (which is attached
 to this post) will be mapped and for the other one I get the warning:
 unknown molecule SOL with ...
 Do I need to create separate mapping files and combine them or it can be
 done just by using unique mixture.xml file. I will appreciate it if you
 can help me with this.

 P.S. I am using the same molecule names as in my atomistic topology file

 Bests,
 Hossein

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[votca] compiling votca in cygwin

[Sikandar Mashayak]

Hi

I am trying to compile votca csg in cygwin using build.sh. However, it is
not able to link to gromacs libraries and giving following error:

checking for module 'libgmx'
--   found libgmx, version 4.6.1
-- Looking for GromacsVersion in /opt/gromacs/lib/libgmx.a;/usr/lib/libm.a
-- Looking for GromacsVersion in /opt/gromacs/lib/libgmx.a;/usr/lib/libm.a
- not found
CMake Error at CMakeModules/FindGROMACS.cmake:84 (message):
  Could not find GromacsVersion in
/opt/gromacs/lib/libgmx.a;/usr/lib/libm.a,
  take look at the error message in
  /home/Sikandar/Apps/Votca/src/csg/CMakeFiles/CMakeError.log to find out
  what was going wrong.  If you don't have pkg-config installed you will
most
  likely have to set GROMACS_LIBRARY and GROMACS_DEP_LIBRARY by hand which
  sets the gromacs lib and it's depencies (i.e.
  -DGROMACS_LIBRARY='/path/to/libgmx.so'
  -DGROMACS_DEP_LIBRARIES='/path/to/libblas.so;/path/to/libm.so') !
Call Stack (most recent call first):
  src/libcsg/CMakeLists.txt:23 (find_package)

error log file is also attached.

Thanks
Sikandar

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CMakeError.log
Description: Binary data

Re: [votca] Convergence problem

[Sikandar Mashayak]

Hi
Soree Kim

To answer your question I am taking example of spce water coarse-graining
by ibi, as in tutorial.

To check for convergence in rdf you can specify following options

cg
non-bonded
---
---
inverse
 ---
---
 post_addconvergence/post_add
 post_add_options
  convergence
  whatdist/what
  weight1.0/weight
  /convergence
/post_add_options
---
---
/inverse
/non-bonded

inverse
---
convergence_checkdefault/convergence_check
convergence_check_options
limit0.001/limit
/convergence_check_options
---
/inverse
/cg

with the above options at each step of ibi, new rdf (dist) would be
computed and
for convergence check the 1-st norm of ( CG-CG.dist.new - CG-CG.dist.tgt)
will be computed
and compared against the limit to decide whether to stop iteration or not.

Now, about the limit value, it depends on what level of accuracy you want
from cg potentials.
To get an idea you can check what is this value at diiferent steps of ibi
of spce in tutorial and decide on
what would be good enough value for your case.

thanks
sikandar

On Mon, Jul 30, 2012 at 7:29 AM, Soree Kim ksr...@gmail.com wrote:

 Thank you for your answer.
 However, I think I didn't ask clearly.
 When I said 'cut-off', it means the value of the convergence.

 convergence_checkdefault/convergence_check
 convergence_check_options
 limit0.001/limit   This value!
 name_glob*.conv/name_glob
 /convergence_check_options

 I want to know how small the limit should be to obtain reasonable rdf.
 And the first question is also about the calculation of that convergence
 value.
 Thank you.

 Soree Kim.

 2012년 7월 27일 금요일 오후 7시 33분 13초 UTC+9, Victor Rühle 님의 말:

 Hey,

 by default, the iterations stop after the maximum number of iterations
 has been reached. If you want a real convergence check, e.g. if the
 distributions match, you will have to add that to your options.xml. In
 particular, check the options

 cg.inverse.convergence_check.**type
 and also add convergence to postadd.

 I just realized the documentation on that is not very good and I had
 to lookup in the code again. I will add a section to the manual.

 About the cutoff: there are different oppinions on how to best choose
 the cutoff. It depends on the system, we usually choose where the RDF
 has a maximum (- minimum in the potential) and is already close to
 one. For water that was around 0.9nm, for methanol around 1.54. You
 can check the tutorials to get a feeling for the values we had chosen.
 As far as I know there is no general way.

 Victor

 2012/7/27 Soree Kim ksr...@gmail.com:
  Hi,
  I want to know how the VOTCA program calculates the convergence.
  And what value is the reasonable cut-off?
  Thank you.
 
  Soree Kim.
 
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Re: [votca] parallel analysis

[Sikandar Mashayak]

Hi  Konstantin

I think, I get your point. I am just restating what you said,
to make sure I understand it right.

Yes, parallelization algorithm used in VOTCA is trivially parallel,
as multiple frames are processed simultaneously by different cores, and
averages are computed in the end once all cores finish their computation.
If the computations performed each frame are  not intensive then
performance is mainly limited by I/O of frame reading.

Would MPI-enabling make sense if per frame analysis is
computationally intensive, and required number of frames
to process are quite large? In that case, it would be useful
to use as many possible nodes offered by HPC cluster, keeping
the same trivially parallel algorithm.

Thanks
Sikandar

On Mon, Apr 23, 2012 at 3:55 PM, Konstantin Koschke 
konstantin.kosc...@gmail.com wrote:

 Cheers guys,

 On Mon, Apr 23, 2012 at 5:33 PM, Christoph Junghans jungh...@votca.org
 wrote:
  Hi  Sikandar,
 
  you are correct!
 
  Threads make use of the shared memory nature of the system and hence
  data is not communicated.
 
  I guess it would be possible to replace the thread class with a
  mpi-based class, but I am not sure how much work it is.
  Maybe Konstantin can comment on this!
 
  Cheers,
 
  Christoph
 
 
  Am 23. April 2012 08:31 schrieb Sikandar Mashayak symasha...@gmail.com
 :
  Hi
 
  As per my understanding, votca applications are thread enabled allowing
  us to use multiple cores on the same machine. Since, the implementation
  is based on the shared memory, I am not sure if we can use it on HPC
  to make use of multiple nodes, which require implementation based on the
  distributed memory.
 
  Please correct me, if I am missing anything.
 
  Thanks
  Sikandar
 

 Threads are limited to shared memory architectures and VOTCA is based
 on threads, thus, you're right.
 Adding MPI as a communication interface is in principle possible.
 However, I don't see a practical application and feel free to correct
 me here:
 - VOTCA uses a simple parallelization over time frames, i.e., if you
 wanted to analyze a trajectory, you could also split it up into chunks
 of the size frames/cores and you'd be able to compute your
 quantities in a trivially parallel way
 - on a current server node with 8-12 cores, this runs already into IO
 limits: in order to use all CPU power, you want to decrease IO (little
 input data) and increase FLOPS (complicated inner calculation loops);
 if your actual calculation is too simple, VOTCA will be limited by
 transferring data from the disk to the memory (IO limit); this is what
 I observe most of the time
 - if you were to generalize this approach to more heterogeneous
 architectures (Threads+MPI), you'd be hitting fast-interconnect limits

 Do you have a minimal example that you'd like to be sped up? The first
 step would be to make sure that your calculation is limited by the
 CPU.

 Best
 Konstantin

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Re: [votca] Coarse grained interactions

[Sikandar Mashayak]

Hey
Rakhee

Since, I have never used VOTCA to do bonded potential coarse-graining
along with non-bonded interactions, my suggestions may be incomplete.
So I request other experienced members of the group to complete
my suggestions or correct me if I made any mistake.

I suggest the following steps,

1. Compute target RDFs and potential of mean forces from your
AMBER simulations.

2. Invert PMFs to get CG bonded interactions.

3. Then you need to do IBI coarse-graining of non-bonded interactions
For that you need to create some GROMACS specific files.  These are
mainly

   1. initial CG configuration file specified as *.gro
   2. Topology file *.top specifying CG bonded and nonbonded
interaction settings
   3. MD simulation parameter file specified as *.mdp
   4. the default table.xvg file

you should go through tutorial files of votca to get an idea about how
these files
look and go through gromacs manual. Information about how to set up
user specified tabulated
   potentials in gromacs can be found at
   http://www.gromacs.org/Documentation/How-tos/Tabulated_Potentials

Since, I have not worked with AMBER suite, i am not sure whether it is
possible to directly
convert from AMBER format files to GROMACS files. Efforts required to
generate GROMACS specific files for coarse-graining would depend upon
the complexity of your reference system.

Or alternative would be to set up your reference simulations itself in the
GROMACS and then use
standard VOTCA tools to do mapping n stuff.
 This option, I guess would require similar efforts as in generating CG set
up files.

cheers
sikandar


On Wed, Feb 8, 2012 at 12:11 PM, rp rakheep...@gmail.com wrote:

 Dear Votca Users,

 I have my atomistic simulations done in using AMBER MD suite. In the
 Votca manual this mention on use of GROMACS trajectory and input
 file.
 I want derive the non bonded potentials using iterative Boltzmann
 inversion and bonded interactions using potential of mean force of
 the
 CG degrees of freedom. Can anyone give me some more information on the
 input files required for the procedure or where I can find some
 related examples.
 Can I work with the parameter and coordinate files used by AMBER.

 Thanks for suggestions
 Rakhee

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[votca] linking to mpi enabled gromacs

[Sikandar Mashayak]

Hi

I am trying to install Votca with mpi enabled gromacs. And it is not able
to link to
gromacs since library file name of gromacs is libgmx_mpi.

So, could anyone please suggest how to link to _mpi libraries of gromacs?

thank you,
sikandar

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Re: [votca] linking to mpi enabled gromacs

[Sikandar Mashayak]

Hey Christoph thanks for the explanation.

As I am not much familiar with cmake, I wonder if I were to use mpic++
instead of g++
how should I specify that? Make any changes to Cmake files?

thanks
sikandar

On Sat, Nov 26, 2011 at 4:44 PM, Christoph Junghans jungh...@votca.orgwrote:

 Am 26. November 2011 14:26 schrieb Sikandar Mashayak symasha...@gmail.com
 :
  I am trying to install Votca with mpi enabled gromacs. And it is not
 able to
  link to
  gromacs since library file name of gromacs is libgmx_mpi.
  So, could anyone please suggest how to link to _mpi libraries of gromacs?
 Short answer: don't do it, just compile gromacs twice (with and without
 mpi).
 Long answer: You could specify
 -DGROMACS_LIBRARIES=/path/to/libgmx_mpi.so, but as libgmx_mpi.so
 contains calls to libmpi.so, you will need to add libmpi.so to
 GROMACS_DEP_LIBRARIES and have to use mpic++ instead of g++ as
 compiler, but as VOTCA make no use of mpi anyway, just link against
 libgmx.so (without mpi).

 Btw, in gromacs only mdrun make use of mpi, all other program run in
 serial and if you only run of shared memory systems mdrun with threads
 is the better option.

 Cheers,

 Christoph


 
  thank you,
  sikandar
 
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[votca] inverse log file gromacs output

[Sikandar Mashayak]

Hi

I notice that when gromacs commands are executed using inverse script with
logging enabled, gromacs command output such as its help, available options,
run time etc. everything is written into the log file. Is there any way that
I could avoid it so that log file would look much more clean?

thanks
sikandar

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Re: [votca] upgrading gromacs version

[Sikandar Mashayak]

Hey Victor

Thanks for suggestions.

cheers
sikandar

On Wed, Sep 28, 2011 at 4:36 AM, Victor Ruehle rue...@votca.org wrote:

 Hey,

 I would advise you to recompile VOTCA against the new Gromacs version.
 That has two reasons:

 1) The Gromacs .tpr files contain a version number, the old version
 might not be able to open newer files anymore
 2) Even though it's dynamic linking, the interface of the libgmx might
 have changed. This could lead to unexpected results and crashes (In
 principle there are version numbers for libraries, however, for a
 software which is ongoing rapid development like gromacs, this might
 not be as strict).

 So 1) would work if you leave the old installation at it's place. If
 you compile against the new version, make sure cmake catches the
 correct path to new version. You might have to delete the
 CMakeCache.txt file in csg.

 Best,
 Victor

 2011/9/27 Sikandar Mashayak symasha...@gmail.com:
  Hi
 
  I plan to upgrade the version of gromacs on my machine. So, I wonder do I
  need to make any changes in Votca installation so that it can find
  appropriate gromacs binaries and libraries?
 
  thanks
  sikandar
 
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Re: [votca] IBI- convergence check

[Sikandar Mashayak]

Hey thanks Christoph.

On Fri, Sep 16, 2011 at 11:48 AM, Christoph Junghans jungh...@votca.orgwrote:

 Hi,

 at this point we only have the type default.

 Cheers,

 Christoph



 2011/9/16 Sikandar Mashayak symasha...@gmail.com:
  Hi
 
  I am trying to specify convergence criteria for IBI coarse-graining.
  According to the manual, it can be specified as
 
  inverse
  ...
  ...
  convergence_check
   # type of convergence check to do
  /convergence_check
 
  convergence_check_options
  limit 0.0001 /limit
  /convergence_check_options
 
  I am not sure what are the types of convergence checks available, and
 what
  need to be specified in that field?
 
  thanks
  sikandar
 
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[votca] CG site for charged group of atoms

[Sikandar Mashayak]

Hey

I am not very sure whether its good idea or bad, to define a CG site for
group of atoms whose net charge is not zero? Does anyone have any thoughts
about it?

thanks
sikandar

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Re: [votca] FM for partially known CG pot

[Sikandar Mashayak]

Hey Victor

I was able to use template.c to write out new trr with error forces. Also,
it may be useful for me to modify csg_map to generate output trajectory in
.trr format with force information, I will give it a try whenever possible.
Right now, as I said earlier, I need to do fmatch on error forces. As you
suggested, I am trying to use *--trj-force *option to accomplish that. But
when I try to download updated csg source code and compile it I get the
errors. I have attached the build log file . Can you please help me with
that

thanks
sikandar

On Sat, Apr 2, 2011 at 2:10 AM, Victor Ruehle rue...@votca.org wrote:

 Check e.g. in csg_map.cc
 (http://doxygen.votca.googlecode.com/hg/csg__map_8cc_source.html)

 string out = foo.trr;
 _writer = TrjWriterFactory().Create(out);
 if(_writer == NULL)
throw runtime_error(output format not supported:  + out);
 _writer-Open(out);
 _writer-Write(top);
 _writer-Close();
 delete _writer;

 You can access topology class to make changes
 (http://doxygen.votca.googlecode.com/hg/classvotca_1_1csg_1_1Topology.html
 )

 2011/4/2 Sikandar Mashayak symasha...@gmail.com:
  yeah, I have been using template.cc for doing post-processing the
  trajectories, but I am used to writing the analyzed data in ascii format,
  not sure how to generate .trr format files with modified data... looking
  into xtc gromacs library...  your input on this will be helpful...
  thanks
  sikandar
 
  On Fri, Apr 1, 2011 at 5:20 PM, Victor Ruehle rue...@votca.org wrote:
 
  if i understood correctly what you mean with error force (=force
  difference) then yes.
 
  I made changes and options should be available now. Please reinstall
  csg (either stable or developer version from repositories). Tarballs
  are not yet updated.
 
  I'm not aware of any gromacs tool which does it. However that would be
  a perfect exercise to get startet with votca development :) It's 3
  additional lines in the template.cc. I can help you to get started.
 
  Victor
 
  2011/4/1 Sikandar Mashayak symasha...@gmail.com:
   yeah sure it helps.. just to be sure that I understand it correctly
   when --traj ref.trr --trj-force cg.trr is used with csg_fmatch then it
   computes the difference between forces on cg site in ref.trr and
 cg.trr
   and
   use error forces as a target force to be matched using the CG
 potentials
   with given options..
   right?
   also, is there any gromacs utility can be used to compute force
   difference
   between two .trr with same positions and generate new .trr with error
   force?
   thanks
   sikandar
  
   On Thu, Mar 31, 2011 at 4:09 PM, Victor Ruehle rue...@votca.org
 wrote:
  
   sorry, sure it is --trj. This will generate a mapped trajectory. Then
   you have to calculate forces using gromacs mdrun -rerun giving a
   coarse-grained topology which contains forces you already know. To
   summarize - csg_map will generate a coarse-grained trajectory from
   atomistic one (only positions), mdrun -rerun adds forces
  
   on csg_fmatch --trj-force (mixed it up --force-trj was wrong):
   indeed, it seems like i forgot to merge that into the stable/default
   branch. Will fix it by tomorrow and let you know when done.
  
   on testing:
   With --trj-force you can specify a coarse-grained trajectory whose
   forces are subtracted before force fitting procedure. If you now put
   in the potentials obtained in a previous forcematching step, these
 are
   subtracted - the forces which are fitted should be zero (the fit
   depends on specified interactions, if you don't change these it
 should
   give identical results, since these are already subtracted - zero).
   This is good to check whether your setup of coarse-grained topology
 is
   correct (interactions specified correctly) and all steps I mentioned
   went fine.
  
   Hope that helped.
  
   Cheers,
   Victor
  
   2011/3/31 Sikandar Mashayak symasha...@gmail.com:
Also, when running the command
csg_map --in traj.trr --out traj_cg.trr --cg mapping.xml
i get error  unknown option --in and when I do it usual way i.e.
csg_map
--top top.tpr --traj traj.trr --out out.trr I get the .trr file but
it
has
zero forces/no force information.
   
   
On Thu, Mar 31, 2011 at 11:38 AM, Sikandar Mashayak
symasha...@gmail.com
wrote:
   
Hey
I may need a bit more explanation to understand last two points
 you
make..
- csg_fmatch --trj traj.trr --force-trj traj_rerun_cg.trr (fill
 give
error force)
::- will the output of this be .trr file with error forces or CG
potential
which reproduces error forces. Also I don't see the --force-trj
option
in
help text/manual for csg_fmatch.
You could test whether you did it correct be using force-matching
potentials as input for rerun - error force should vanish
This point is not clear.
thanks
sikandar
On Thu, Mar 31, 2011 at 11:19 AM, Victor Ruehle rue...@votca.org
 
wrote:
   
Hey
   
unless

Re: [votca] FM for partially known CG pot

[Sikandar Mashayak]

Also, when running the command

csg_map --in traj.trr --out traj_cg.trr --cg mapping.xml

i get error  unknown option --in and when I do it usual way i.e. csg_map
--top top.tpr --traj traj.trr --out out.trr I get the .trr file but it has
zero forces/no force information.



On Thu, Mar 31, 2011 at 11:38 AM, Sikandar Mashayak symasha...@gmail.comwrote:

 Hey

 I may need a bit more explanation to understand last two points you make..

 *- csg_fmatch --trj traj.trr --force-trj traj_rerun_cg.trr (fill give*
 *error force)*
 *
 *
 *::-* will the output of this be .trr file with error forces or CG
 potential which reproduces error forces. Also I don't see the --force-trj
 option in help text/manual for csg_fmatch.

 *You could test whether you did it correct be using force-matching*
 *potentials as input for rerun - error force should vanish*
 *
 *
 This point is not clear.

 thanks
 sikandar

 On Thu, Mar 31, 2011 at 11:19 AM, Victor Ruehle rue...@votca.org wrote:

 Hey

 unless you change your basis set for cg force field (cut-off, add
 interactions, etc) or add some bias to fit procedure (extension to
 code needed), you will probably end up with identical potentials as
 doing only force matching.

 However, technically  it can be done the following:
 - csg_map --in traj.trr --out traj_cg.trr --cg mapping.xml (same for
 conf.gro)
 - prepare coarse-grained topolology with already known potentials
 - mdrun -rerun traj_cg.trr   (trajectory will contain knowledge based
 forces)
 - csg_fmatch --trj traj.trr --force-trj traj_rerun_cg.trr (fill give
 error force)

 You could test whether you did it correct be using force-matching
 potentials as input for rerun - error force should vanish

 Victor

 2011/3/31 Sikandar Mashayak symasha...@gmail.com:
  Hi
  Another similar situation I am thinking of is like follow ::
  1. I have full atomistic trajectory and forces as a target system.
  2. I want to Coarse-Grain and determine CG-CG potential. I also have
 some
  knowledge what this CG-CG looks like and and insist on using this
  information. To do that I plan to do following.
  3. Use this knowledge based ( so to call) CG-CG to perform MD-Rerun with
  full atomistic trajectories and get CG forces.
  4.  Now compute the error in forces on CG site for full MD and CG
 MD-rerun.
  5. Use this error force as target force to do Force-Matching and get an
  estimate for CG-CG potential which reproduces this error.
  6. Finally add this error CG potential to original (knowledge based)
  potential to get more accurate CG-CG potential.
 
  So the question I have is, how do I generate trajectories for just error
  forces. I mean , is there any way I use two gromacs trajectories and get
 new
  trajectory with error force?
  thanks
  sikandar
 
  On Mon, Mar 28, 2011 at 5:35 PM, Sikandar Mashayak 
 symasha...@gmail.com
  wrote:
 
  thanks victor, I will see how subtracting known parts and setting
 interval
  to the unknown range will work out.. i guess good starting point would
 be
  check this out with simple 12-6 LJ case...
  ---
  sikandar
 
  On Wed, Mar 23, 2011 at 6:13 PM, Victor Ruehle rue...@votca.org
 wrote:
 
  Hmm, don't see any clean way how to do this with the current
  implementation. One might be able to subtract the known parts (which
  can be calculated using rerun) using --force-trj and setting the
  interval only to the unknown region. However this might lead to kinks
  due to interpolation effects at the crossing.
 
  The clean way would require extending the code.
 
  2011/3/15 Sikandar Mashayak symasha...@gmail.com:
   Hey
   I am thinking of a problem where I have some physical understanding
 or
   constraint for CG-CG potential that I want to parameterize. So that,
 I
   know
   say from 0-r1 what is CG-CG potential values and want to determine
   values
   from r1-rcut.
   Is there any way I can set up such Force Matching calculations in
   Votca?
   thanks
   sikandar
  
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[votca] FM for partially known CG pot

[Sikandar Mashayak]

Hey

I am thinking of a problem where I have some physical understanding or
constraint for CG-CG potential that I want to parameterize. So that, I know
say from 0-r1 what is CG-CG potential values and want to determine values
from r1-rcut.

Is there any way I can set up such Force Matching calculations in Votca?

thanks
sikandar

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Re: [votca] Force Matching F_CG

[Sikandar Mashayak]

Hey
Victor

Thanks for clarification. But I am worried about not using constraints
during simulation. If my definition of molecule requires to apply
constraint, like using Settle for SPC/E water, then how can I remove them.
Also, why is this condition? Is it because that Gromacs writes the forces to
trajectory before applying any constraints, which effectively change the
actual force acting on the atoms?

thanks
sikandar

On Thu, Mar 10, 2011 at 5:10 PM, Victor Ruehle rue...@votca.org wrote:

 Hey,

 VOTCA does not compute atomistic forces, they need to be provided in
 the atomistic trr file (just switch on writing forces in gromacs). You
 should do same output frequency for forces as for coordinates. So you
 can do it while running or use rerun to calculate forces for an
 existing trajectory.

 The coarse-grained forces are then calculated according to the mapping
 weights in the cg molecule definition.

 Some things to consider:
  - make sure you don't use constraints during simulation
  - be sure what you are doing if not using a center of mass mapping

 For more details see the paper by Noid et al:
 http://jcp.aip.org/resource/1/jcpsa6/v128/i24/p244114_s1

 Cheers,
 Victor

 2011/3/10 Sikandar Mashayak symasha...@gmail.com:
  Hi
  Force matching algorithm tries to solve the eqn. 2.20 in the manual. So
 for
  given set of CG force parameters, how does it compute the forces on CG
 site
  using full atomistic MD trajectory?
  To do that I usually perform mdrun -rerun with mdp and topology files
  designed for CG system. Is csg_fmatch doing the same?
  thanks
  sikandar
 
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[votca] Force Matching F_CG

[Sikandar Mashayak]

Hi

Force matching algorithm tries to solve the eqn. 2.20 in the manual. So for
given set of CG force parameters, how does it compute the forces on CG site
using full atomistic MD trajectory?

To do that I usually perform mdrun -rerun with mdp and topology files
designed for CG system. Is csg_fmatch doing the same?

thanks
sikandar

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Re: [votca] Table Potentials MD

[Sikandar Mashayak]

Hey Sebastian

thanks for the explanation.. yeah I just realised it should have been mailed
to Gromacs mailing list rather than VOTCA.


cheers
sikandar
On Wed, Nov 24, 2010 at 3:21 AM, Sebastian Fritsch 
frit...@mpip-mainz.mpg.de wrote:

 Hi Sikander,


 this is actually a gromacs question and should be on the gromacs list :-)
 Anyway, I think gromacs takes the forces as they are from the table (an
 interpolates for intermediate values) for the simulation, which is why your
 struct. properties do not change. Your total potential energy however is
 probably wrong. Also you should see a warning at the beginning of the
 simulation if your force deviates from the potential given in the table.


 Cheers
 Sebastian

 Hi

 I have a doubt regarding use of table in CG MD Simulations. When one uses
 table for pair potentials to perform Coarse-Grained MD simulations in
 Gromacs, one specifies  potential as well as force values in table. Does
 Gromacs actually use the force values from the table or it just uses
 potential values and then differentiate it to compute force on its own?

 This may sound weird question, but I have lately observed that, if I
 change the forces in table keeping the potential values to be the same, I
 get the same structural properties such as density profile in nano-channel.

 thanks
 sikandar
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