On Thu, Apr 12, 2018 at 2:28 PM, Alexander Alexander
<alexanderwie...@gmail.com> wrote:
>
> Thank you.
>
> An then these parameter
> <pot_max>10000000</pot_max>
> <table_end>4.0</table_end>
> which usually comes in the very end of settings.xml of IBI in the <inverse>
> section, are again mx of potential and end of it, which should be larger
> than all our end table in each section.
Like I said, these are parameter for the gromacs table (the xvg file),
not the VOTCA table (the pot.new file).
You could set them differently for each table, but usually the values
above should work for most Gromacs runs.

>
> On Thursday, April 12, 2018 at 4:09:27 PM UTC-4, Christoph Junghans wrote:
>>
>> On Thu, Apr 12, 2018 at 2:03 PM, Alexander Alexander
>> <alexand...@gmail.com> wrote:
>> >
>> > Hi Christoph,
>> >
>> > I guess I found out what do you mean, I hope the attached bonded tables
>> > for
>> > 3-bead system would be fine.
>> Yeah these one look better, if you zoom around the minimum you should
>> see some structure for the Boltzmann inversion.
>
>
> Yes, when I zoom in them, I see a wide U shape for each of bonded
> interactions as in attachment.
> Now, to use them in IBI (only nonbonded), should I use the zoomed version of
> them or these are fine for IBI over nonbonded?
If you are doing only non-bonded IBI, just provide VOTCA with the full
table_a1.xvg, table_b1.xvg etc. and add them to <filelist> as well.
Also don't forget to remove the <bonded> sections of the interactions
you aren't iterating from your settings.xml file.

Christoph
>
> Thank you.
> Regards,
> Alex
>>
>>
>> Christoph
>> >
>> > Best regards,
>> > Alex
>> >
>> >
>> > On Thursday, April 12, 2018 at 1:26:37 PM UTC-4, Alexander Alexander
>> > wrote:
>> >>
>> >>
>> >> Thanks.
>> >>
>> >> On Thursday, April 12, 2018 at 12:43:54 PM UTC-4, Christoph Junghans
>> >> wrote:
>> >>>
>> >>> On Thu, Apr 12, 2018 at 9:57 AM, Alexander Alexander
>> >>> <alexand...@gmail.com> wrote:
>> >>> >
>> >>> >
>> >>> > On Thursday, April 12, 2018 at 8:14:42 AM UTC-4, Christoph Junghans
>> >>> > wrote:
>> >>> >>
>> >>> >> On Thu, Apr 12, 2018 at 3:39 AM, Alexander Alexander
>> >>> >> <alexand...@gmail.com> wrote:
>> >>> >> >
>> >>> >> > Hi,
>> >>> >> >
>> >>> >> > I was wondering if it is normal to have table_b1,2,3,4.xvg like
>> >>> >> > the
>> >>> >> > attached
>> >>> >> > figures? They are the result if BI (similar script as hexane
>> >>> >> > example)
>> >>> >> > over a
>> >>> >> > 500 ns nvt simulation of a single molecule. What could be the
>> >>> >> > meaning of
>> >>> >> > the
>> >>> >> > straight line passing from point (0,0) in table_b1.xvg for
>> >>> >> > example?
>> >>> >> No they don't look normal, bonded interaction should always look
>> >>> >> like
>> >>> >> an modified U with both sides, left and right, going to infinity.
>> >>> >
>> >>> >
>> >>> > I do not know what exactly I am doing wrong; I guess the 500 ns NVT
>> >>> > simulation is fine to get statistic for a single molecule, and then
>> >>> > I
>> >>> > am
>> >>> > following these command in the hexane example for to obtain
>> >>> > bonded.xvg
>> >>> > potential using BI:
>> >>> >
>> >>> > #!/bin/bash -e
>> >>> >
>> >>> > #calculate bonded potentials with csg_boltzmann
>> >>> >
>> >>> > csg_boltzmann --top prdnvt.tpr --trj prdnvt.trr --cg mapp.xml
>> >>> > --begin
>> >>> > 2000 <
>> >>> > boltzmann_cmds
>> >>> >
>> >>> > #smooth bonded potentials
>> >>> > csg_call --sloppy-tables table smooth bond-LG-H1.pot.ib
>> >>> > input_bond-LG-H1.pot
>> >>> > csg_call --sloppy-tables table smooth bond-H1-H2.pot.ib
>> >>> > input_bond-H1-H2.pot
>> >>> > csg_call --sloppy-tables table smooth bond-H2-L.pot.ib
>> >>> > input_bond-H2-L.pot
>> >>> > csg_call --sloppy-tables table smooth bond-L-RG.pot.ib
>> >>> > input_bond-L-RG.pot
>> >>> > csg_call --sloppy-tables table smooth angle-LG-H1-H2.pot.ib
>> >>> > input_angle-LG-H1-H2.pot
>> >>> > csg_call --sloppy-tables table smooth angle-H1-H2-L.pot.ib
>> >>> > input_angle-H1-H2-L.pot
>> >>> > csg_call --sloppy-tables table smooth angle-H2-L-RG.pot.ib
>> >>> > input_angle-H2-L-RG.pot
>> >>> > csg_call --sloppy-tables table smooth dihedral-LG-H1-H2-L.pot.ib
>> >>> > input_dihedral-LG-H1-H2-L.pot
>> >>> > csg_call --sloppy-tables table smooth dihedral-H1-H2-L-RG.pot.ib
>> >>> > input_dihedral-H1-H2-L-RG.pot
>> >>> >
>> >>> > #convert bonded potentials to GROMACS tables
>> >>> > if [ -d table ]; then
>> >>> >   rm -r table
>> >>> > fi
>> >>> > mkdir table
>> >>> >
>> >>> > csg_call --ia-type bond --ia-name bond-LG-H1 --options
>> >>> > bond-LG-H1.xml
>> >>> > convert_potential gromacs --clean input_bond-LG-H1.pot
>> >>> > table/table_b1.xvg
>> >>> > csg_call --ia-type bond --ia-name bond-H1-H2 --options
>> >>> > bond-H1-H2.xml
>> >>> > convert_potential gromacs --clean input_bond-H1-H2.pot
>> >>> > table/table_b2.xvg
>> >>> > csg_call --ia-type bond --ia-name bond-H2-L --options bond-H2-L.xml
>> >>> > convert_potential gromacs --clean input_bond-H2-L.pot
>> >>> > table/table_b3.xvg
>> >>> > csg_call --ia-type bond --ia-name bond-L-RG --options bond-L-RG.xml
>> >>> > convert_potential gromacs --clean input_bond-L-RG.pot
>> >>> > table/table_b4.xvg
>> >>> > csg_call --ia-type angle --ia-name angle-LG-H1-H2 --options
>> >>> > angle-LG-H1-H2.xml convert_potential gromacs --clean
>> >>> > input_angle-LG-H1-H2.pot table/table_a1.xvg
>> >>> > csg_call --ia-type angle --ia-name angle-H1-H2-L --options
>> >>> > angle-H1-H2-L.xml
>> >>> > convert_potential gromacs --clean input_angle-H1-H2-L.pot
>> >>> > table/table_a2.xvg
>> >>> > csg_call --ia-type angle --ia-name angle-H2-L-RG --options
>> >>> > angle-H2-L-RG.xml
>> >>> > convert_potential gromacs --clean input_angle-H2-L-RG.pot
>> >>> > table/table_a3.xvg
>> >>> > csg_call --ia-type angle --ia-name dihedral-LG-H1-H2-L --options
>> >>> > dihedral-LG-H1-H2-L.xml convert_potential gromacs --clean
>> >>> > input_dihedral-LG-H1-H2-L.pot table/table_d1.xvg
>> >>> > csg_call --ia-type angle --ia-name dihedral-H1-H2-L-RG --options
>> >>> > dihedral-H1-H2-L-RG.xml convert_potential gromacs --clean
>> >>> > input_dihedral-H1-H2-L-RG.pot table/table_d2.xvg
>> >>> >
>> >>> > Even I have similar problem for a molecule with three beads.
>> >>> > Attachment is a log.txt file out of running the above script. Any
>> >>> > help
>> >>> > would
>> >>> > be highly appreciated.
>> >>> As discussed on the mailing list in great detail, the art is to pick
>> >>> the min and max of the potentials, so that the extrapolation is
>> >>> useful.
>> >>
>> >> You mean I have to edit (clip) the pot.in I get from csg_boltzmann (tab
>> >> ....) (the first command in the above script), as bond-case.pot.in,
>> >> right?
>> >>  Actually, that is the point I am getting confused.
>> >> There are several min and max set in input files:
>> >> One min and max set is in csg_boltzmann such as:
>> >> tab set min XXX
>> >> tab set max YYY
>> >>
>> >> One is in one set of min max in the <bonded> section of bond-A-B.xml
>> >> feed
>> >> to the csg_call. like:
>> >> <bonded>
>> >>      <min>xxx</min>
>> >>      <max>yyy</max>
>> >>      <step>0.001</step>
>> >> </bonded>
>> >> Again there is another set of min max in the <inverse> section of the
>> >> same
>> >> file as below:
>> >> <inverse>
>> >>                 <gromacs>
>> >>                         <pot_max>1e8</pot_max>
>> >>                         <table_end>0.4</table_end>
>> >>                         <table_bins>0.001</table_bins>
>> >>                 </gromacs>
>> >> </inverse>
>> >>
>> >>> You can basically not expect VOTCA will get this right automatically.
>> >>> And nothing prevents you from doing this by hand, right? You are
>> >>> right.
>> >>> And then you can provide your hand-tuned initial guess as a pot.in
>> >>> file
>> >>> to IBI.
>> >>
>> >> Probably you mean rest of BI (like csg_call and converting to
>> >> table_*.xvg
>> >> format), because I still getting the bonded potentials using BI. And
>> >> the
>> >> final table_*.xvg are supposed be used as input for IBI.
>> >>
>> >> Best regards,
>> >> Alex
>> >>>
>> >>>
>> >>> Christoph
>> >>>
>> >>> >
>> >>> > BTW, how the form of the angle-bonded potential should look like?
>> >>> > The
>> >>> > table_a1.xvg for hexane does not go to +infinity from the right leg.
>> >>> > Thank you.
>> >>> > Regards,
>> >>> > Alex
>> >>> >
>> >>> >>
>> >>> >> > Also, is the format of the table_bonded.xvg is "x y [error bar]"?
>> >>> >> x,y, force - see the gromacs manual for details.
>> >>> >>
>> >>> >> Christoph
>> >>> >>
>> >>> >> > Thank you.
>> >>> >> > Regards,
>> >>> >> > Alex
>> >>> >> >
>> >>> >> > On Wednesday, April 11, 2018 at 3:44:30 PM UTC-4, Christoph
>> >>> >> > Junghans
>> >>> >> > wrote:
>> >>> >> >>
>> >>> >> >> On Wed, Apr 11, 2018 at 12:49 PM, Alexander Alexander
>> >>> >> >> <alexand...@gmail.com> wrote:
>> >>> >> >> >
>> >>> >> >> > Hi Christoph,
>> >>> >> >> >
>> >>> >> >> > On Wednesday, April 11, 2018 at 8:22:24 AM UTC-4, Christoph
>> >>> >> >> > Junghans
>> >>> >> >> > wrote:
>> >>> >> >> >>
>> >>> >> >> >>
>> >>> >> >> >>
>> >>> >> >> >> On Wed, Apr 11, 2018, 01:51 Alexander Alexander
>> >>> >> >> >> <alexand...@gmail.com>
>> >>> >> >> >> wrote:
>> >>> >> >> >>>
>> >>> >> >> >>>
>> >>> >> >> >>> Hi,
>> >>> >> >> >>> You mean BI over a single molecule in vacuum?
>> >>> >> >> >>
>> >>> >> >> >>
>> >>> >> >> >> Yes, or any potential, which has right equilibrium
>> >>> >> >> >> length/value.
>> >>> >> >> >
>> >>> >> >> > I decided to the BI for bonded interaction, the procedure and
>> >>> >> >> > results
>> >>> >> >> > for
>> >>> >> >> > one of the molecule is shared in the below link, I am not sure
>> >>> >> >> > if
>> >>> >> >> > everything
>> >>> >> >> > is fine, I would be so appreciated if you could kindly have a
>> >>> >> >> > look
>> >>> >> >> > and
>> >>> >> >> > give
>> >>> >> >> > any suggestion, please.
>> >>> >> >> >
>> >>> >> >> >
>> >>> >> >> >
>> >>> >> >> > https://drive.google.com/open?id=1hvIH9mk1LfYo5LOO1VjBAkBZx7L0q3P0
>> >>> >> >> >
>> >>> >> >> > Also, do the settings used in the hexane or spce water example
>> >>> >> >> > in
>> >>> >> >> > the
>> >>> >> >> > tutorial are the real settings and parameters used in your
>> >>> >> >> > publication?
>> >>> >> >> > or
>> >>> >> >> > these are just examples.
>> >>> >> >> Most of them are, but some got adapted a bit to be more
>> >>> >> >> instructive
>> >>> >> >> as
>> >>> >> >> tutorials.
>> >>> >> >>
>> >>> >> >> Christoph
>> >>> >> >> >
>> >>> >> >> > Thanks.
>> >>> >> >> > Regards,
>> >>> >> >> > Alex
>> >>> >> >> >>
>> >>> >> >> >>
>> >>> >> >> >>>
>> >>> >> >> >>> Instead of sd integrater can md integrator (but still in NVT
>> >>> >> >> >>> ensemble)
>> >>> >> >> >>> be
>> >>> >> >> >>> used in IBI ( bonded and nonbonded or either of them) and
>> >>> >> >> >>> still
>> >>> >> >> >>> have
>> >>> >> >> >>> good
>> >>> >> >> >>> results?
>> >>> >> >> >>
>> >>> >> >> >>
>> >>> >> >> >> Sure as long as you are still sampling NVT you can use any
>> >>> >> >> >> integrator.
>> >>> >> >> >> However, usually sd is the more stable integrator, so I don't
>> >>> >> >> >> think
>> >>> >> >> >> that
>> >>> >> >> >> change will help with your problem.
>> >>> >> >> >>
>> >>> >> >> >> Christoph
>> >>> >> >> >>
>> >>> >> >> >>> Thanks,
>> >>> >> >> >>> Alex
>> >>> >> >> >>>
>> >>> >> >> >>> --
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>> >>> >> >>
>> >>> >> >>
>> >>> >> >> --
>> >>> >> >> Christoph Junghans
>> >>> >> >> Web: http://www.compphys.de
>> >>> >> >
>> >>> >> > --
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>> >>> >>
>> >>> >> --
>> >>> >> Christoph Junghans
>> >>> >> Web: http://www.compphys.de
>> >>> >
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>> >>>
>> >>>
>> >>> --
>> >>> Christoph Junghans
>> >>> Web: http://www.compphys.de
>> >
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>>
>> --
>> Christoph Junghans
>> Web: http://www.compphys.de
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