On Sun, Jun 7, 2020 at 7:16 AM Rajat Gupta <rajatgpt911...@gmail.com> wrote: > > Thank you for the help, Christoph. > > I tried making the changes suggested (Scale = 10; kBT=1) but I got the > following error at step_001: > > ERROR: Lost atoms: original 4096 current 0 (src/thermo.cpp:439) > Last command: run 10000 > > I am attaching my settings.xml and input file (sc.in) for reference. > > Since my target RDF is also in reduced units (generated using LAMMPS), unlike > gromacs units which was in spce-ibi_lammps tutorial, I next tried making > changes by keeping the scale=1 (since both target RDF and lammps have same > reduced units) and this time the lammps simulations ran but I got error while > rdf calculations in step_001:
That won't work, let me repeat what I said in my last email: VOTCA will scale the positions read from the dump file with a factor of 0.1 (as VOTCA assumes dumps are in Angstroms, but works in nm internally). However, the target rdf is compared against the rdf calculated by csg_stat (in nm) hence the target rdf needs to be in nm as well, meaning scaled by 0.1 the units of the dump files. To summarize, if your simulation is in reduced units, which VOTCA reads from a dump file and then scales by 0.1, the target rdf needs to be scaled by 0.1 from the reduced units as well. Same for the number in settings.xml, they need to be scaled by 0.1 from your reduced units. And that would also explain "The max of interaction "CG-CG" bigger is than half the box." error below as the max is too big by a factor 10. Christoph > > > Calculating rdfs with csg_stat using 4 tasks > Running critical command 'csg_stat --nt 4 --options > /home/rajat/Desktop/Inverse_Design/settings.xml --top input.data --trj > traj.dump --begin 0 --first-frame 0' > begin to calculate distribution functions > # of bonded interactions: 0 > # of non-bonded interactions: 1 > > WARNING: The votca lammps data reader is only able to read lammps files > formatted in the following styles: > angle > atom > bond > full > molecule > > These styles use the following formats in the atom block: > atom-ID molecule-ID atom-type charge x y z > atom-ID molecule-ID atom-type charge x y z nx ny nz > atom-ID molecule-ID atom-type x y z > atom-ID molecule-ID atom-type x y z nx ny nz > atom-ID atom-type x y z > atom-ID atom-type x y z nx ny nz > . > . > . > I have 4096 beads in 4096 molecules > > Reading frame, timestep 10000 > an error occurred: > The max of interaction "CG-CG" bigger is than half the box. > > Callstack: > /home/rajat/share/votca/scripts/inverse/inverse.sh - linenumber 266 > do_external - linenumber 176 in > /home/rajat/share/votca/scripts/inverse/functions_common.sh > /home/rajat/share/votca/scripts/inverse/update_ibi.sh - linenumber 31 > for_all - linenumber 22 (see 'csg_call --cat function for_all') > do_external - linenumber 19 (see 'csg_call --cat function > do_external') > > /home/rajat/share/votca/scripts/inverse/calc_rdf_generic.sh - linenumber 84 > critical - linenumber 4 (see 'csg_call --cat > function critical') > die - linenumber 2 (see 'csg_call --cat > function die') > > I'm trying to perform IBI calculations for a simple cubic lattice. Is there > anything that I'm missing or doing wrong? > > Any help is appreciated. > > Thanks, > Rajat > > On Sunday, May 31, 2020 at 5:43:48 PM UTC+5:30, Christoph Junghans wrote: >> >> >> >> On Sun, May 31, 2020, 05:47 Rajat Gupta <rajatgp...@gmail.com> wrote: >>> >>> Hello everyone, >>> >>> I am new to using VOTCA and have some queries. I am working in coarse >>> graining using VOTCA and used LAMMPS to generate my target RDF (in reduced >>> units). >>> >>> While going through ibi_lammps tutorial in VOTCA, I saw the unit conversion >>> done for LAMMPS real units. >>> >>> Can anyone please suggest me the changes I need to make in my >>> "settings.xml" in order to perform IBI calculations and handle the lj units? >> >> VOTCA always assumes lammps files are in angstroms even if they are in LJ >> units and then converts them to it's internal units, nm. And writes the rdf >> and potentials out in nm as well. >> That means for a setup in LJ units the potential will be in LJ*(angstroms to >> nm conversion) [0.1]. >> Hence you a basically just have to scale the potential back to LJ units by >> scaling everything with a factor 10 using the "scale" parameter in the >> settings file. That covers the x axis, for the y axis you just have to set >> the 'kBT' parameter to the right unitless value for the temperature you are >> calculating. kBT is the only unit parameter used in ibi. >> >> Christoph >>> >>> >>> Thanks, >>> Rajat >>> >>> -- >>> 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 vo...@googlegroups.com. >>> To view this discussion on the web visit >>> https://groups.google.com/d/msgid/votca/0466c098-1257-4075-9b4d-91aa67dd2228%40googlegroups.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 votca+unsubscr...@googlegroups.com. > To view this discussion on the web visit > https://groups.google.com/d/msgid/votca/a143a7e5-441a-43cb-bd93-34c4d1a6da14o%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. 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