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 <javascript:>> 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 <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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