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):
-----------------------
<non-bonded>
<!-- name of the interaction -->
<name>CG1-CG1</name>
<!-- types involved in this interaction -->
<type1>CG1</type1>
<type2>CG1</type2>
<!-- dimension + grid spacing of tables for calculations -->
<min>0</min>
<max>1.66</max>
<step>0.005</step>
<re>
<!-- function>cbspl or lj126</function-->
<function>cbspl</function>
<cbspl>
<nknots>84</nknots>
<core>extrapolate</core>
</cbspl>
</re>
<inverse>
<!-- target distribution (rdf), just give gromas rdf.xvg -->
<target>TCH-TCH.dist.tgt</target>
<!-- update cycles -->
<!--do_potential>1</do_potential-->
<do_potential>1 0 0</do_potential>
<!-- additional post processing of dU before added to potential -->
<!--post_update></post_update-->
<post_update>smooth</post_update>
<!-- some options for the post update scripts -->
<post_update_options>
<!--scale>0.10</scale-->
<smooth>
<iterations>3</iterations>
</smooth>
</post_update_options>
<!-- additional post processing of U after dU added to potential -->
<!--post_add>acc_convergence average</post_add-->
<post_add>acc_convergence average</post_add>
<post_add_options>
<!-- convergence check options -->
<convergence>
<!-- for RE we check change in potentials/parameters (new-cur) -->
<what>pot</what>
<weight>1.0</weight>
<base>cur</base>
<norm>2</norm>
</convergence>
<average>
<what>param pot</what>
</average>
</post_add_options>
<!-- name of the table for gromacs run -->
<gromacs>
<table>table_CG1_CG1.xvg</table>
</gromacs>
</inverse>
</non-bonded>
-----------------------
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 <
> [email protected] <javascript:>> 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 <[email protected]>
>>> wrote:
>>>
>>>> On Mon, Jul 23, 2018 at 9:28 AM, 'Andrey Brukhno' via votca
>>>> <[email protected]> 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
>>>> >>>> <non-bonded>
>>>> >>>> ...
>>>> >>>> <post_update>lj</post_update>
>>>> >>>> <post_update_options>
>>>> >>>> <lj>
>>>> >>>> <c6> LJ C6 Value </c6>
>>>> >>>> <c12> LJ C12 Value </c12>
>>>> >>>> </lj>
>>>> >>>> </post_update_options>
>>>> >>>> ...
>>>> >>>> </non-bonded>
>>>> >>>>
>>>> >>>> I hope this helps.
>>>> >>>>
>>>> >>>> Best,
>>>> >>>> Sikandar
>>>> >>>>
>>>> >>>> On Thu, Jul 19, 2018 at 6:13 PM Christoph Junghans <
>>>> [email protected]>
>>>> >>>> wrote:
>>>> >>>>>
>>>> >>>>>
>>>> >>>>>
>>>> >>>>> On Thu, Jul 19, 2018 at 18:15 'Andrey Brukhno' via votca
>>>> >>>>> <[email protected]> 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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>>>> >>>>>> For more options, visit https://groups.google.com/d/optout.
>>>> >>>>>
>>>> >>>>> --
>>>> >>>>> Christoph Junghans
>>>> >>>>> Web: http://www.compphys.de
>>>> >>>>>
>>>> >>>>> --
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>>>> >
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>>>>
>>>>
>>>> --
>>>> Christoph Junghans
>>>> Web: http://www.compphys.de
>>>>
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>>>>
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<<attachment: CG-reupdate-test.zip>>
