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.

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 <javascript:>> 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?

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 
> >>> >> >> >>> 
> >>> >> >> >>> -- 
> >>> >> >> >>> 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. 
> >>> >> >> > 
> >>> >> >> > -- 
> >>> >> >> > 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 
> >>> >> > 
> >>> >> > -- 
> >>> >> > 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 
> >>> > 
> >>> > -- 
> >>> > 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 
> > 
> > -- 
> > 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 <javascript:>. 
> > To post to this group, send email to vo...@googlegroups.com 
> <javascript:>. 
> > 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 
>

-- 
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+unsubscr...@googlegroups.com.
To post to this group, send email to votca@googlegroups.com.
Visit this group at https://groups.google.com/group/votca.
For more options, visit https://groups.google.com/d/optout.

Reply via email to