On Thu, Apr 12, 2018 at 2:03 PM, Alexander Alexander <[email protected]> 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.
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 >>> <[email protected]> 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 >>> >> <[email protected]> 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 >>> >> >> <[email protected]> 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 >>> >> >> >> <[email protected]> >>> >> >> >> 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 [email protected]. >>> >> >> >>> To post to this group, send email to [email protected]. >>> >> >> >>> 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 [email protected]. >>> >> >> > To post to this group, send email to [email protected]. >>> >> >> > 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 [email protected]. >>> >> > To post to this group, send email to [email protected]. >>> >> > 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 [email protected]. >>> > To post to this group, send email to [email protected]. >>> > 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 [email protected]. > To post to this group, send email to [email protected]. > 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 [email protected]. To post to this group, send email to [email protected]. Visit this group at https://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
