On Thu, Apr 12, 2018 at 11:26 AM, Alexander Alexander <[email protected]> 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> There is the region were the update is performed.
> 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> The max. y-value for the potential > <table_end>0.4</table_end> Where the gromacs table is ending, which isn't necessarily the same as <max>. > <table_bins>0.001</table_bins> The spacing of the gromacs table. For more details see the VOTCA manual: http://doc.votca.org/manual.pdf sec 10.4 Christoph > </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. 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