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. 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