Hi Christoph,

I guess I found out what do you mean, I hope the attached bonded tables for 
3-bead system would be fine.

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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>> >> >> > 
>> >> >> > -- 
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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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