2013/7/24 <[email protected]>:
>
>
> W dniu środa, 24 lipca 2013 13:36:04 UTC+1 użytkownik [email protected]
> napisał:
>>
>> I am also trying to iteratively get distribution for 1 of my interactions
>> leaving other 14 being fully repulsive.... My potential at step 124 has a
>> much deeper minima than the initial one... And ditribution is much higher
>> than the target one obviously... These beads of which potential i am trying
>> to get stay in a globular conformation...There must be something wrong..
>> Please, see attached my files, any help appreciated.
>>
>> Steven
>>
>
> It is absolutely ridiculous... I used the cut off of 0.4 to refine this one
> potential as a trial and with comparing to my target distribution it was
> underestimated... so what Votca did? Exactly opposite... I looked at the
> next steps and the distributions are even smaller...!!! Fantastic!
This was your 1st strike out of three. Please clam down and mind your words!
So far you have never been able to show me that VOTCA did something
wrong. Like for all other simulation packages, for VOTCA the
garbage-in-garbage-out principle applies, too. VOTCA is deterministic,
it can only handle inputs it was made for and it cannot make
scientific decisions for you. If you give it unexpected input
("garbage"), it will most likely not turn it into gold.
Btw. VOTCA is open-source, if you don't like how it is working, feel
free to change the code. (but remember to call your derived code
differently!)
Victor, Tristan, Sikandar, me and all the other developers are
providing technical support on a voluntary and free of charge basis.
All that said, let's come back to your question.
The target distribution distribution is something you give as an
input, VOTCA does nothing else than putting is on the same grid as the
interaction and even that can be prevented if you provide it with the
right grid already. To check that compare step_*/NAME.dist.tgt with
whatever you put in the main directory.
Your distribution looks artificially high and I am not sure where this
is coming from. You could try running g_rdf in one of the step to see
if csg_stat does something wrong, but I doubt that the normalization
is just the standard shell volume:
<https://code.google.com/p/votca/source/browse/src/tools/csg_stat_imc.cc?repo=csg&name=stable#383>
>
>>
>>
>>
>> W dniu wtorek, 23 lipca 2013 20:05:45 UTC+1 użytkownik Christoph Junghans
>> napisał:
>>>
>>> 2013/7/23 <[email protected]>:
>>> >
>>> >
>>> > W dniu wtorek, 23 lipca 2013 16:24:25 UTC+1 użytkownik Christoph
>>> > Junghans
>>> > napisał:
>>> >>
>>> >> 2013/7/23 <[email protected]>:
>>> >> > Another example which seems to be correct but wish to know, please
>>> >> > see
>>> >> > attached. The derivative (last column) of function H(x) is zero
>>> >> > while
>>> >> > H(x)
>>> >> > is highly positive... Is that correct potential?
>>> >> I don't see a problem here, the begin of the potential is constant and
>>> >> hence the derivative is zero.
>>> >>
>>> >> > My protein still stays in a
>>> >> > globular conformation and I corrected other potentials. If it is ok
>>> >> > would
>>> >> > you try to make IBI with potentials one by one?
>>> >> do_potential in the xml file allows you to divide interactions into
>>> >> group to update only one group at the time.
>>> >> The default will put all interactions in one group.
>>> >>
>>> >> I would approximate your 4 special interactions by a non-linear
>>> >> spring-like potential (see my earlier email) and keep them fixed for
>>> >> now and do IBI on the other 11 interactions.
>>> >
>>> >
>>> > The problem is that all 15 of my distributions goes to zero as there is
>>> > nothing at large distances. I already have angles take from atomistic
>>> > simulations, by one boltzmann inversion I got great results (tabulated
>>> > angles). Now I shifted my distributions to RDF = 1 which option 1. Then
>>> > I
>>> > should use:
>>> > for the 1st potential
>>> > potentia.update 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0
>>> > for the second
>>> > potential.update 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0
>>> > etc. am I right?
>>> Yes!
>>>
>>> >
>>> > The other option would be to to use the non-linear spring as for bonded
>>> > (you
>>> > mentioned before). Does only Votca 1.3 supports it? Is there any
>>> > tutorial?
>>> > Which option would you recommend?
>>> I meant to Boltzmann invert the distribution and use it as
>>> table_bX.xvg and keep it fixed.
>>> But it will depend on your system if this approach will work or not.
>>>
>>>
>>> >
>>> > Steven
>>> >
>>> >
>>> >>
>>> >>
>>> >>
>>> >> >
>>> >> > Steven
>>> >> >
>>> >> > W dniu wtorek, 23 lipca 2013 10:22:26 UTC+1 użytkownik
>>> >> > [email protected]
>>> >> > napisał:
>>> >> >>
>>> >> >> Could you please also explain me why from attached potential Votca
>>> >> >> produce
>>> >> >> a table with negative (close to zero) values at low distances? It
>>> >> >> does
>>> >> >> not
>>> >> >> make sense and hence my protein remains globular... I have 4
>>> >> >> potentials
>>> >> >> like
>>> >> >> this out of 15...
>>> >> >>
>>> >> >> Steven
>>> >> >>
>>> >> >> W dniu poniedziałek, 22 lipca 2013 23:40:50 UTC+1 użytkownik
>>> >> >> Christoph
>>> >> >> Junghans napisał:
>>> >> >>>
>>> >> >>> 2013/7/22 <[email protected]>:
>>> >> >>> >
>>> >> >>> >
>>> >> >>> > On Friday, July 19, 2013 8:02:01 PM UTC+1, Christoph Junghans
>>> >> >>> > wrote:
>>> >> >>> >>
>>> >> >>> >> 2013/7/19 <[email protected]>:
>>> >> >>> >> > 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.
>>> >> >>> >> VOTCA always shifts the potential, to U(r_max)=0 for non-bonded
>>> >> >>> >> interaction and U_min=0 for bonded interactions.
>>> >> >>> >> This is why I said making VOTCA believe your interaction is
>>> >> >>> >> bonded,
>>> >> >>> >> might
>>> >> >>> >> help.
>>> >> >>> >> The update rule is the same for bonded and non-bonded.
>>> >> >>> >>
>>> >> >>> >> Anyhow the shift doesn't change the physics, so why are you so
>>> >> >>> >> bother
>>> >> >>> >> about it? You could just to do IBI and shift the finial outcome
>>> >> >>> >> once
>>> >> >>> >> it is converged.
>>> >> >>> >>
>>> >> >>> >> Christoph
>>> >> >>> >
>>> >> >>> >
>>> >> >>> > Thank you. This what I will do - shift the final potential. what
>>> >> >>> > would
>>> >> >>> > be
>>> >> >>> > the best cut off for IBI - is that the place where distributions
>>> >> >>> > have
>>> >> >>> > maxima?
>>> >> >>> That is a tricky question, to be honest I don't know. You might
>>> >> >>> have
>>> >> >>> to play with the cutoff a bit.
>>> >> >>>
>>> >> >>> >
>>> >> >>> >
>>> >> >>> > Steven
>>> >> >>> >
>>> >> >>> >
>>> >> >>> >>
>>> >> >>> >> >
>>> >> >>> >> > Steven
>>> >> >>> >> >
>>> >> >>> >> > W dniu środa, 17 lipca 2013 17:43:51 UTC+1 użytkownik
>>> >> >>> >> > Christoph
>>> >> >>> >> > Junghans
>>> >> >>> >> > napisał:
>>> >> >>> >> >>
>>> >> >>> >> >> 2013/7/17 <[email protected]>:
>>> >> >>> >> >> > 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 <[email protected]>:
>>> >> >>> >> >> >> >
>>> >> >>> >> >> >> >
>>> >> >>> >> >> >> > 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,
>>> >> >>> >> >> >> >> <[email protected]>
>>> >> >>> >> >> >> >> 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 <[email protected]>:
>>> >> >>> >> >> >> >> >> > 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
>>> >> >>> >> >> >> >> >> do.
>>> >> >>> >> >> >> >> >>
>>> >> >>> >> >> >> >> >> First, have a look at your ACI-ACI.dist.tgt again,
>>> >> >>> >> >> >> >> >> this
>>> >> >>> >> >> >> >> >> distribution
>>> >> >>> >> >> >> >> >> doesn't go to one hence the potential doesn't go to
>>> >> >>> >> >> >> >> >> 0
>>> >> >>> >> >> >> >> >> for
>>> >> >>> >> >> >> >> >> large
>>> >> >>> >> >> >> >> >> r.
>>> >> >>> >> >> >> >> >> And that is mainly the reason why VOTCA cannot
>>> >> >>> >> >> >> >> >> handle
>>> >> >>> >> >> >> >> >> it,
>>> >> >>> >> >> >> >> >> ACI-ACI.dist.tgt is not a common rdf!
>>> >> >>> >> >> >> >> >> You will have to provide an initial guess (pot.in)
>>> >> >>> >> >> >> >> >> to
>>> >> >>> >> >> >> >> >> make
>>> >> >>> >> >> >> >> >> it
>>> >> >>> >> >> >> >> >> work.
>>> >> >>> >> >> >> >> >> (Please also read my email from July 10th again.)
>>> >> >>> >> >> >> >> >>
>>> >> >>> >> >> >> >> >> Second, VOTCA does exactly what it is supposed to
>>> >> >>> >> >> >> >> >> do.
>>> >> >>> >> >> >> >> >> Go
>>> >> >>> >> >> >> >> >> into
>>> >> >>> >> >> >> >> >> gnuplot
>>> >> >>> >> >> >> >> >> and
>>> >> >>> >> >> >> >> >> run:
>>> >> >>> >> >> >> >> >> p [0:3][-20:5] "ACI-ACI.dist.tgt" u
>>> >> >>> >> >> >> >> >> 1:(-2.49435*log($2)-5.7) w
>>> >> >>> >> >> >> >> >> l,
>>> >> >>> >> >> >> >> >> "ACI-ACI.pot.cur" w l
>>> >> >>> >> >> >> >> >> Except for some small deviations, which come from
>>> >> >>> >> >> >> >> >> the
>>> >> >>> >> >> >> >> >> cubic
>>> >> >>> >> >> >> >> >> spline
>>> >> >>> >> >> >> >> >> interpolation, there is no difference in the
>>> >> >>> >> >> >> >> >> curves.
>>> >> >>> >> >> >> >> >> As Victor said before, VOTCA shifts the potential
>>> >> >>> >> >> >> >> >> to be
>>> >> >>> >> >> >> >> >> zero
>>> >> >>> >> >> >> >> >> at
>>> >> >>> >> >> >> >> >> the
>>> >> >>> >> >> >> >> >> cutoff -> -10.433 - 5.7 = -16.1. This shift of 5.7
>>> >> >>> >> >> >> >> >> makes
>>> >> >>> >> >> >> >> >> no
>>> >> >>> >> >> >> >> >> difference
>>> >> >>> >> >> >> >> >> for the thermodynamics however.
>>> >> >>> >> >> >> >> >>
>>> >> >>> >> >> >> >> >> Third, even pot.new is correct. Run
>>> >> >>> >> >> >> >> >> $ paste ACI-ACI.dist.new <(sed '/^#/d'
>>> >> >>> >> >> >> >> >> ACI-ACI.dist.tgt)
>>> >> >>> >> >> >> >> >> <(sed
>>> >> >>> >> >> >> >> >> '/^#/d'
>>> >> >>> >> >> >> >> >> ACI-ACI.pot.cur) > ACI-ACI.temp
>>> >> >>> >> >> >> >> >> to generate a temp file.
>>> >> >>> >> >> >> >> >> And go into gnuplot and plot:
>>> >> >>> >> >> >> >> >> p [0:3][-20:5] "ACI-ACI.temp" u
>>> >> >>> >> >> >> >> >> 1:(2.49435*log($2/$5)+$8-16.1)
>>> >> >>> >> >> >> >> >> w
>>> >> >>> >> >> >> >> >> l,
>>> >> >>> >> >> >> >> >> "ACI-ACI.pot.new" w l
>>> >> >>> >> >> >> >> >> There is basically no difference in the curves.
>>> >> >>> >> >> >> >> >>
>>> >> >>> >> >> >> >> >> Conclusion:
>>> >> >>> >> >> >> >> >> - check your distributions again
>>> >> >>> >> >> >> >> >> - provide pot.in for the interaction, which don't
>>> >> >>> >> >> >> >> >> have
>>> >> >>> >> >> >> >> >> a
>>> >> >>> >> >> >> >> >> "common"
>>> >> >>> >> >> >> >> >> rdf
>>> >> >>> >> >> >> >> >> (meaning which doesn't go to 1)
>>> >> >>> >> >> >> >> >>
>>> >> >>> >> >> >> >> >> Christoph
>>> >> >>> >> >> >> >> >>
>>> >> >>> >> >> >> >> >>
>>> >> >>> >> >> >> >> >> >
>>> >> >>> >> >> >> >> >> >
>>> >> >>> >> >> >> >> >> >
>>> >> >>> >> >> >> >> >> >
>>> >> >>> >> >> >> >> >> > W dniu poniedziałek, 15 lipca 2013 12:59:40 UTC+1
>>> >> >>> >> >> >> >> >> > użytkownik
>>> >> >>> >> >> >> >> >> > [email protected] napisał:
>>> >> >>> >> >> >> >> >> >>
>>> >> >>> >> >> >> >> >> >>
>>> >> >>> >> >> >> >> >> >>
>>> >> >>> >> >> >> >> >> >> W dniu poniedziałek, 15 lipca 2013 12:42:37
>>> >> >>> >> >> >> >> >> >> UTC+1
>>> >> >>> >> >> >> >> >> >> użytkownik
>>> >> >>> >> >> >> >> >> >> Victor
>>> >> >>> >> >> >> >> >> >> Rühle
>>> >> >>> >> >> >> >> >> >> napisał:
>>> >> >>> >> >> >> >> >> >>>
>>> >> >>> >> >> >> >> >> >>> Dear Steven,
>>> >> >>> >> >> >> >> >> >>>
>>> >> >>> >> >> >> >> >> >>> provided the same kBT was used, I can think of
>>> >> >>> >> >> >> >> >> >>> two
>>> >> >>> >> >> >> >> >> >>> issues
>>> >> >>> >> >> >> >> >> >>> which
>>> >> >>> >> >> >> >> >> >>> might
>>> >> >>> >> >> >> >> >> >>> lead to these differences
>>> >> >>> >> >> >> >> >> >>>
>>> >> >>> >> >> >> >> >> >>> 1) votca can shift the potential, but the shape
>>> >> >>> >> >> >> >> >> >>> should
>>> >> >>> >> >> >> >> >> >>> match.
>>> >> >>> >> >> >> >> >> >>> That
>>> >> >>> >> >> >> >> >> >>> can
>>> >> >>> >> >> >> >> >> >>> in
>>> >> >>> >> >> >> >> >> >>> particular happen if you cut the rdf in a
>>> >> >>> >> >> >> >> >> >>> region
>>> >> >>> >> >> >> >> >> >>> where
>>> >> >>> >> >> >> >> >> >>> there
>>> >> >>> >> >> >> >> >> >>> are
>>> >> >>> >> >> >> >> >> >>> still
>>> >> >>> >> >> >> >> >> >>> modulations.
>>> >> >>> >> >> >> >> >> >>> 2) What type of potential are you lookin at?
>>> >> >>> >> >> >> >> >> >>> For
>>> >> >>> >> >> >> >> >> >>> bonds
>>> >> >>> >> >> >> >> >> >>> and
>>> >> >>> >> >> >> >> >> >>> angles,
>>> >> >>> >> >> >> >> >> >>> there
>>> >> >>> >> >> >> >> >> >>> is indeed a normalization necessary, see
>>> >> >>> >> >> >> >> >> >>>
>>> >> >>> >> >> >> >> >> >>>
>>> >> >>> >> >> >> >> >> >>>
>>> >> >>> >> >> >> >> >> >>>
>>> >> >>> >> >> >> >> >> >>>
>>> >> >>> >> >> >> >> >> >>>
>>> >> >>> >> >> >> >> >> >>>
>>> >> >>> >> >> >> >> >> >>>
>>> >> >>> >> >> >> >> >> >>>
>>> >> >>> >> >> >> >> >> >>> http://dx.doi.org/10.1002/(SICI)1521-4044(199802)49:2/3<61::AID-APOL61>3.0.CO;2-V
>>> >> >>> >> >> >> >> >> >>
>>> >> >>> >> >> >> >> >> >>
>>> >> >>> >> >> >> >> >> >> Thank you. I am looking at the nonbonded
>>> >> >>> >> >> >> >> >> >> interactions
>>> >> >>> >> >> >> >> >> >> only.
>>> >> >>> >> >> >> >> >> >> The
>>> >> >>> >> >> >> >> >> >> shape
>>> >> >>> >> >> >> >> >> >> of
>>> >> >>> >> >> >> >> >> >> the potential matches but the minima is lower
>>> >> >>> >> >> >> >> >> >> than
>>> >> >>> >> >> >> >> >> >> from
>>> >> >>> >> >> >> >> >> >> my
>>> >> >>> >> >> >> >> >> >> calulation.
>>> >> >>> >> >> >> >> >> >> There
>>> >> >>> >> >> >> >> >> >> is no normalization for non bonded so this is
>>> >> >>> >> >> >> >> >> >> weird.
>>> >> >>> >> >> >> >> >> >> I
>>> >> >>> >> >> >> >> >> >> cut
>>> >> >>> >> >> >> >> >> >> it
>>> >> >>> >> >> >> >> >> >> at
>>> >> >>> >> >> >> >> >> >> the
>>> >> >>> >> >> >> >> >> >> begining as there were very small values and
>>> >> >>> >> >> >> >> >> >> Votca
>>> >> >>> >> >> >> >> >> >> was
>>> >> >>> >> >> >> >> >> >> not
>>> >> >>> >> >> >> >> >> >> able
>>> >> >>> >> >> >> >> >> >> to
>>> >> >>> >> >> >> >> >> >> extrapolate it properly.
>>> >> >>> >> >> >> >> >> >>
>>> >> >>> >> >> >> >> >> >>>
>>> >> >>> >> >> >> >> >> >>>
>>> >> >>> >> >> >> >> >> >>> Your second point indeed sounds a bit weired.
>>> >> >>> >> >> >> >> >> >>> Could
>>> >> >>> >> >> >> >> >> >>> you
>>> >> >>> >> >> >> >> >> >>> please
>>> >> >>> >> >> >> >> >> >>> post
>>> >> >>> >> >> >> >> >> >>> these
>>> >> >>> >> >> >> >> >> >>> few curves to help debugging (i.e. the
>>> >> >>> >> >> >> >> >> >>> <name>.pot.cur,
>>> >> >>> >> >> >> >> >> >>> <name>.pot.new
>>> >> >>> >> >> >> >> >> >>> <name>.dist.tgt <name>.dist.new of the
>>> >> >>> >> >> >> >> >> >>> iteration 1
>>> >> >>> >> >> >> >> >> >>> folder)?
>>> >> >>> >> >> >> >> >> >>>
>>> >> >>> >> >> >> >> >> >>> Victor
>>> >> >>> >> >> >> >> >> >>
>>> >> >>> >> >> >> >> >> >>
>>> >> >>> >> >> >> >> >> >> Please, see attached.
>>> >> >>> >> >> >> >> >> >>
>>> >> >>> >> >> >> >> >> >>
>>> >> >>> >> >> >> >> >> >>>
>>> >> >>> >> >> >> >> >> >>>
>>> >> >>> >> >> >> >> >> >>>
>>> >> >>> >> >> >> >> >> >>> 2013/7/15 <[email protected]>
>>> >> >>> >> >> >> >> >> >>>>
>>> >> >>> >> >> >> >> >> >>>> Dear Votca Users,
>>> >> >>> >> >> >> >> >> >>>>
>>> >> >>> >> >> >> >> >> >>>> I have to issues with IBI:
>>> >> >>> >> >> >> >> >> >>>>
>>> >> >>> >> >> >> >> >> >>>> 1) I took one my ditributions and calculated
>>> >> >>> >> >> >> >> >> >>>> on my
>>> >> >>> >> >> >> >> >> >>>> own
>>> >> >>> >> >> >> >> >> >>>> potential
>>> >> >>> >> >> >> >> >> >>>> W=
>>> >> >>> >> >> >> >> >> >>>> -kBT
>>> >> >>> >> >> >> >> >> >>>> ln(RDF) and I got different potential than
>>> >> >>> >> >> >> >> >> >>>> Votca
>>> >> >>> >> >> >> >> >> >>>> provide
>>> >> >>> >> >> >> >> >> >>>> me.
>>> >> >>> >> >> >> >> >> >>>> For
>>> >> >>> >> >> >> >> >> >>>> instance
>>> >> >>> >> >> >> >> >> >>>> lets calculate the potential minimum for the
>>> >> >>> >> >> >> >> >> >>>> distribution
>>> >> >>> >> >> >> >> >> >>>> maximum
>>> >> >>> >> >> >> >> >> >>>> of
>>> >> >>> >> >> >> >> >> >>>> 162.
>>> >> >>> >> >> >> >> >> >>>> Pot = -.249435*ln(164) = -12.69. The minimum
>>> >> >>> >> >> >> >> >> >>>> of
>>> >> >>> >> >> >> >> >> >>>> Votca
>>> >> >>> >> >> >> >> >> >>>> potential
>>> >> >>> >> >> >> >> >> >>>> corresponds
>>> >> >>> >> >> >> >> >> >>>> to approximately -16 kJ/mol. Where I missed
>>> >> >>> >> >> >> >> >> >>>> something? is
>>> >> >>> >> >> >> >> >> >>>> it
>>> >> >>> >> >> >> >> >> >>>> somehow
>>> >> >>> >> >> >> >> >> >>>> normalized?
>>> >> >>> >> >> >> >> >> >>>>
>>> >> >>> >> >> >> >> >> >>>> 2) After 1st iteration my distribution was
>>> >> >>> >> >> >> >> >> >>>> much
>>> >> >>> >> >> >> >> >> >>>> higher
>>> >> >>> >> >> >> >> >> >>>> than
>>> >> >>> >> >> >> >> >> >>>> the
>>> >> >>> >> >> >> >> >> >>>> target
>>> >> >>> >> >> >> >> >> >>>> one so I guess the potential should decrease
>>> >> >>> >> >> >> >> >> >>>> but
>>> >> >>> >> >> >> >> >> >>>> apparently
>>> >> >>> >> >> >> >> >> >>>> the
>>> >> >>> >> >> >> >> >> >>>> new
>>> >> >>> >> >> >> >> >> >>>> potential has deeper minima so the next
>>> >> >>> >> >> >> >> >> >>>> distribution
>>> >> >>> >> >> >> >> >> >>>> has
>>> >> >>> >> >> >> >> >> >>>> a
>>> >> >>> >> >> >> >> >> >>>> even
>>> >> >>> >> >> >> >> >> >>>> higer
>>> >> >>> >> >> >> >> >> >>>> distribution. Could anyone please explain me
>>> >> >>> >> >> >> >> >> >>>> this?
>>> >> >>> >> >> >> >> >> >>>>
>>> >> >>> >> >> >> >> >> >>>> Steven
>>> >> >>> >> >> >> >> >> >>>>
>>> >> >>> >> >> >> >> >> >>>>
>>> >> >>> >> >> >> >> >> >>>> --
>>> >> >>> >> >> >> >> >> >>>> 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 [email protected].
>>> >> >>> >> >> >> >> >> >>>> To post to this group, send email to
>>> >> >>> >> >> >> >> >> >>>> [email protected].
>>> >> >>> >> >> >> >> >> >>>> Visit this group at
>>> >> >>> >> >> >> >> >> >>>> http://groups.google.com/group/votca.
>>> >> >>> >> >> >> >> >> >>>> For more options, visit
>>> >> >>> >> >> >> >> >> >>>> https://groups.google.com/groups/opt_out.
>>> >> >>> >> >> >> >> >> >>>>
>>> >> >>> >> >> >> >> >> >>>>
>>> >> >>> >> >> >> >> >> >>>
>>> >> >>> >> >> >> >> >> >>>
>>> >> >>> >> >> >> >> >> > --
>>> >> >>> >> >> >> >> >> > 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 [email protected].
>>> >> >>> >> >> >> >> >> > To post to this group, send email to
>>> >> >>> >> >> >> >> >> > [email protected].
>>> >> >>> >> >> >> >> >> > Visit this group at
>>> >> >>> >> >> >> >> >> > http://groups.google.com/group/votca.
>>> >> >>> >> >> >> >> >> > For more options, visit
>>> >> >>> >> >> >> >> >> > https://groups.google.com/groups/opt_out.
>>> >> >>> >> >> >> >> >> >
>>> >> >>> >> >> >> >> >> >
>>> >> >>> >> >> >> >> >>
>>> >> >>> >> >> >> >> >>
>>> >> >>> >> >> >> >> >>
>>> >> >>> >> >> >> >> >> --
>>> >> >>> >> >> >> >> >> Christoph Junghans
>>> >> >>> >> >> >> >> >> Web: http://www.compphys.de
>>> >> >>> >> >> >> >> >
>>> >> >>> >> >> >> >> > --
>>> >> >>> >> >> >> >> > You received this message because you are subscribed
>>> >> >>> >> >> >> >> > to
>>> >> >>> >> >> >> >> > the
>>> >> >>> >> >> >> >> > Google
>>> >> >>> >> >> >> >> > Groups
>>> >> >>> >> >> >> >> > "votca" group.
>>> >> >>> >> >> >> >> > To unsubscribe from this group and stop receiving
>>> >> >>> >> >> >> >> > emails
>>> >> >>> >> >> >> >> > from
>>> >> >>> >> >> >> >> > it,
>>> >> >>> >> >> >> >> > send
>>> >> >>> >> >> >> >> > an
>>> >> >>> >> >> >> >> > email to [email protected].
>>> >> >>> >> >> >> >> > To post to this group, send email to
>>> >> >>> >> >> >> >> > [email protected].
>>> >> >>> >> >> >> >> > Visit this group at
>>> >> >>> >> >> >> >> > http://groups.google.com/group/votca.
>>> >> >>> >> >> >> >> > For more options, visit
>>> >> >>> >> >> >> >> > https://groups.google.com/groups/opt_out.
>>> >> >>> >> >> >> >> >
>>> >> >>> >> >> >> >> >
>>> >> >>> >> >> >> >
>>> >> >>> >> >> >> > --
>>> >> >>> >> >> >> > 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 [email protected].
>>> >> >>> >> >> >> >
>>> >> >>> >> >> >> > To post to this group, send email to
>>> >> >>> >> >> >> > [email protected].
>>> >> >>> >> >> >> > Visit this group at
>>> >> >>> >> >> >> > http://groups.google.com/group/votca.
>>> >> >>> >> >> >> > For more options, visit
>>> >> >>> >> >> >> > https://groups.google.com/groups/opt_out.
>>> >> >>> >> >> >> >
>>> >> >>> >> >> >> >
>>> >> >>> >> >> >>
>>> >> >>> >> >> >>
>>> >> >>> >> >> >>
>>> >> >>> >> >> >> --
>>> >> >>> >> >> >> Christoph Junghans
>>> >> >>> >> >> >> Web: http://www.compphys.de
>>> >> >>> >> >> >
>>> >> >>> >> >> > --
>>> >> >>> >> >> > You received this message because you are subscribed to
>>> >> >>> >> >> > the
>>> >> >>> >> >> > Google
>>> >> >>> >> >> > Groups
>>> >> >>> >> >> > "votca" group.
>>> >> >>> >> >> > To unsubscribe from this group and stop receiving emails
>>> >> >>> >> >> > from
>>> >> >>> >> >> > it,
>>> >> >>> >> >> > send
>>> >> >>> >> >> > an
>>> >> >>> >> >> > email to [email protected].
>>> >> >>> >> >> >
>>> >> >>> >> >> > To post to this group, send email to
>>> >> >>> >> >> > [email protected].
>>> >> >>> >> >> > Visit this group at http://groups.google.com/group/votca.
>>> >> >>> >> >> > For more options, visit
>>> >> >>> >> >> > https://groups.google.com/groups/opt_out.
>>> >> >>> >> >> >
>>> >> >>> >> >> >
>>> >> >>> >> >>
>>> >> >>> >> >>
>>> >> >>> >> >>
>>> >> >>> >> >> --
>>> >> >>> >> >> Christoph Junghans
>>> >> >>> >> >> Web: http://www.compphys.de
>>> >> >>> >> >
>>> >> >>> >> > --
>>> >> >>> >> > You received this message because you are subscribed to the
>>> >> >>> >> > Google
>>> >> >>> >> > Groups
>>> >> >>> >> > "votca" group.
>>> >> >>> >> > To unsubscribe from this group and stop receiving emails from
>>> >> >>> >> > it,
>>> >> >>> >> > send
>>> >> >>> >> > an
>>> >> >>> >> > email to [email protected].
>>> >> >>> >> > To post to this group, send email to [email protected].
>>> >> >>> >> > Visit this group at http://groups.google.com/group/votca.
>>> >> >>> >> > For more options, visit
>>> >> >>> >> > https://groups.google.com/groups/opt_out.
>>> >> >>> >> >
>>> >> >>> >> >
>>> >> >>> >>
>>> >> >>> >>
>>> >> >>> >>
>>> >> >>> >> --
>>> >> >>> >> Christoph Junghans
>>> >> >>> >> Web: http://www.compphys.de
>>> >> >>> >
>>> >> >>> > --
>>> >> >>> > You received this message because you are subscribed to the
>>> >> >>> > Google
>>> >> >>> > Groups
>>> >> >>> > "votca" group.
>>> >> >>> > To unsubscribe from this group and stop receiving emails from
>>> >> >>> > it,
>>> >> >>> > send
>>> >> >>> > an
>>> >> >>> > email to [email protected].
>>> >> >>> > To post to this group, send email to [email protected].
>>> >> >>> > Visit this group at http://groups.google.com/group/votca.
>>> >> >>> > For more options, visit
>>> >> >>> > https://groups.google.com/groups/opt_out.
>>> >> >>> >
>>> >> >>> >
>>> >> >>>
>>> >> >>>
>>> >> >>>
>>> >> >>> --
>>> >> >>> Christoph Junghans
>>> >> >>> Web: http://www.compphys.de
>>> >> >
>>> >> > --
>>> >> > You received this message because you are subscribed to the Google
>>> >> > Groups
>>> >> > "votca" group.
>>> >> > To unsubscribe from this group and stop receiving emails from it,
>>> >> > send
>>> >> > an
>>> >> > email to [email protected].
>>> >> > To post to this group, send email to [email protected].
>>> >> > Visit this group at http://groups.google.com/group/votca.
>>> >> > For more options, visit https://groups.google.com/groups/opt_out.
>>> >> >
>>> >> >
>>> >>
>>> >>
>>> >>
>>> >> --
>>> >> Christoph Junghans
>>> >> Web: http://www.compphys.de
>>> >
>>> > --
>>> > You received this message because you are subscribed to the Google
>>> > Groups
>>> > "votca" group.
>>> > To unsubscribe from this group and stop receiving emails from it, send
>>> > an
>>> > email to [email protected].
>>> > To post to this group, send email to [email protected].
>>> > Visit this group at http://groups.google.com/group/votca.
>>> > For more options, visit https://groups.google.com/groups/opt_out.
>>> >
>>> >
>>>
>>>
>>>
>>> --
>>> Christoph Junghans
>>> Web: http://www.compphys.de
>
> --
> You received this message because you are subscribed to the Google Groups
> "votca" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to [email protected].
> To post to this group, send email to [email protected].
> Visit this group at http://groups.google.com/group/votca.
> For more options, visit https://groups.google.com/groups/opt_out.
>
>
--
Christoph Junghans
Web: http://www.compphys.de
--
You received this message because you are subscribed to the Google Groups
"votca" group.
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