On Tue, Jan 3, 2023 at 9:47 AM Saeed Norouzi <[email protected]> wrote: > > Dear Christoph, > Thank you so much for your help. I used the <table_begin> and <table_end> > in my setting file, and now it works. Could I also do the extrapolation on my > target distribution, so I do not have to do it for every iteration and remove > this interaction-specific from the setting file? That might work, but I am not sure! The problem with poorly sampled regions in IBI is that they can lead to systematic errors in the update.
> Also, How could I have other than linear extrapolation for my data? Yes, there should be an option, inverse.lammps.table_left_exprapolation for each interaction (and same for right), options are constant, linear, quadratic, exponential and sasha. See "csg_call potential extrapolate --help" and "csg_call table extrapolate --help" for details. > Moreover, as you can see below, I have dihedral interaction in my settings > file and I am trying to do ibi for this part also. but the problem is the > VOTCA gives the potential file for dihedral in radian units not degree. I am > using lammps and I need to have the table function in degree units, as VOTCA > does for angle potential. Can you please help me out with this? Dihedrals are not fully implemented yet. But I think you could set inverse.lammps.scale to 180/pi=57.295 for that interaction. Christoph > > <!-- Dihedral Part --> > <bonded> > <!-- name of the interaction --> > <name>dihedral.1</name> > <min>-3.14159</min> > <max>3.14159</max> > <step>0.01</step> > <inverse> > <!-- target distribution --> > <target>dihedral.1.dist.tgt</target> > <lammps> > <table>table_d1.xvg</table> > <table_begin>-3.14159</table_begin> > <table_end>3.14159</table_end> > </lammps> > </inverse> > </bonded> > > > Best regards > Saeed > > > > > > > On Mon, Jan 2, 2023 at 4:16 PM Christoph Junghans <[email protected]> wrote: >> >> On Mon, Jan 2, 2023 at 7:51 AM Saeed Norouzi <[email protected]> wrote: >> > >> > Dear VOTCA Users, >> > >> > I am trying to use ibi for bonded interaction (bond,angle, and dihedral). >> > The problem is when I am using bond distribution we do not have data for >> > some ranges (like for bond distribution in this tutorial), so during the >> > iteration some bonds length is bigger or smaller than the table outer or >> > inner cutoff and I get error in LAMMPS. does anyone has idea what can I do >> > for this error? is there any option in VOTCA to replace the zeros in the >> > probability for bonds with some small values so I can increase the table >> > cutoff or I should do it manually? >> There are interaction-specific properties inverse.lamps.table_begin >> and inverse.lamps.table_end that you can set for each interaction that >> can be smaller/ larger than VOTCA's min and max (the area where IBI is >> performed) . VOTCA will then do an extrapolation for that extra area. >> >> Christoph >> > >> > I am using LAMMPS for my ibi and here is an error I have currently. >> > >> > Per MPI rank memory allocation (min/avg/max) = 7.672 | 7.674 | 7.676 Mbytes >> > Step Time TotEng PotEng Volume Density Temp Press >> > 0 0 963.12455 -1360.1188 151186.66 1.029793 >> > 600 -1094.7381 >> > 2000 20 928.00314 -1457.0206 151186.66 1.029793 >> > 615.95537 -1217.8225 >> > 4000 40 942.24742 -1472.8241 151186.66 1.029793 >> > 623.71551 917.70274 >> > 6000 60 925.95597 -1483.2126 151186.66 1.029793 >> > 622.19103 3122.7127 >> > 8000 80 921.17567 -1446.9757 151186.66 1.029793 >> > 611.59792 1398.679 >> > 10000 100 972.68412 -1498.2288 151186.66 1.029793 >> > 638.13709 3228.6631 >> > 12000 120 968.92421 -1504.366 151186.66 1.029793 >> > 638.75105 2570.6902 >> > 14000 140 973.39445 -1546.9816 151186.66 1.029793 >> > 650.91141 -2645.2069 >> > 16000 160 826.48486 -1573.7195 151186.66 1.029793 >> > 619.87591 164.50872 >> > ERROR on proc 20: Bond length > table outer cutoff: type 3 length >> > 4.4888905 (src/MOLECULE/bond_table.cpp:605) >> > Last command: run 50000 >> > >> > >> > Best regards >> > Saeed >> > >> > -- >> > Join us on Slack: https://join.slack.com/t/votca/signup >> > --- >> > 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 view this discussion on the web visit >> > https://groups.google.com/d/msgid/votca/de34c1df-ca77-466b-a29d-3af382daed5en%40googlegroups.com. >> >> >> >> -- >> Christoph Junghans >> Web: http://www.compphys.de >> >> -- >> Join us on Slack: https://join.slack.com/t/votca/signup >> --- >> 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 view this discussion on the web visit >> https://groups.google.com/d/msgid/votca/CAHG27e5LqWxmX2BZL%2BfOYOCQ-MEQVHZon-c2jpu%3DkByywUZGAA%40mail.gmail.com. > > -- > Join us on Slack: https://join.slack.com/t/votca/signup > --- > 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 view this discussion on the web visit > https://groups.google.com/d/msgid/votca/CAJZjMJbERZcwt5CDFXznUw83UYwFiLGTLFjWeXm%2BpTm2mjQwzw%40mail.gmail.com. -- Christoph Junghans Web: http://www.compphys.de -- Join us on Slack: https://join.slack.com/t/votca/signup --- You received this message because you are subscribed to the Google Groups "votca" group. 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