No, as I see it and I mentioned, the convert_potential lammps command converts the potential into the correct file format and (as discussed) converts the angular potential from rad to deg (ifthe --no-r2d option is not! set), but it will not convert units. So it always matters what the units of the original simulation have been (kj/mol or kcal/mol) The factor 0.239006 converts kj/mol (GROMACS default units) into kcal/mol (LAMMPS units real). .... When converting e.g. the pair potential, you also have to convert then nm (GROMACS default units) into nm (LAMMPS units real) or vice versa or not depending which code you used for the atomistic simulation and which one you will use for the CG simulation.
Best Christoph Am Donnerstag, 25. April 2019 15:20:42 UTC+2 schrieb CHRISTINA-ANNA GATSIOU: > > One additional question. In case I use LAMMPS with real units and I am > performing IBI do I need to add scaling (0.239006) to my ibi settings.xml. > Thanks > Christianna > > On 23 Apr 2019, at 6:23 PM, [email protected] <javascript:> wrote: > > If I see it correctly in > https://github.com/votca/csg/blob/master/share/scripts/inverse/potential_shift.pl#L82, > > for bonded interactions the shift value is determined as the lowest > potential value which e.g. for a quadratic potential would be the minimum: > > for(my $i=0; $i<=$#r; $i++) { > $zero=$dpot[$i] if (($flag[$i] =~ /[i]/) and not defined($zero)); > $zero=$dpot[$i] if (($flag[$i] =~ /[i]/) and ($dpot[$i]<$zero)); > } > > However, in this case the lowest potential value is -47041495963199 at 1.5 > > > > Am Dienstag, 23. April 2019 17:14:35 UTC+2 schrieb Christoph Junghans: >> >> On Tue, Apr 23, 2019 at 9:02 AM <[email protected]> wrote: >> > >> > Hi, >> > >> > as I see it the default --shift option in the table conversion causes >> the problem (it shifts all potential values by the 10^14) factor as you >> have very high forces and thus potential energies at the "left" border of >> your table. >> >> Thanks, that was a good catch! I am wondering isn't the potential for >> angle interactions suppose to shift so that the minimum is at 0? >> Code here: >> >> https://github.com/votca/csg/blob/master/share/scripts/inverse/potential_shift.pl#L82 >> >> >> So where does it go wrong? >> >> Christoph >> > >> > I tried the following commands and it seems to work: >> > >> > >> > csg_call table integrate A-B-A.force A-B-A.pot >> > csg_call table linearop A-B-A.pot A-B-A.pot -1 0 >> > >> > csg_call --ia-type angle --ia-name A-B-A --options >> settings_convert_table_angles.xml convert_potential lammps --no-shift >> --clean A-B-A.pot A-B-A.table >> > >> > with the settings file I attached. >> > >> > The --no-shift option prevents the unwanted shifting. >> > >> > (As I see it, in case you want to run the simulation with lammps you >> should scale your potential file A-B-A.pot before! you call the >> "convert_potential lammps" command as this command outputs the table in the >> right format and converted to degrees, but does not correct for the >> different units in GROMACS and LAMMPS. Though, if you use lammps units real >> (energy kcal/mol, .... )you have to scale the potential values by 0.239006 >> before by e.g. runninh >> > >> > csg_call table linearop A-B-A.pot A-B-A.pot_scaled 0.239006 0 >> > >> > and then running >> > >> > csg_call --ia-type angle --ia-name A-B-A --options >> settings_convert_table_angles.xml convert_potential lammps --no-shift >> --clean A-B-A.pot_scaled A-B-A.table >> > >> > afterwards) >> > >> > Best >> > >> > Christoph >> > >> > >> > >> > Am Donnerstag, 18. April 2019 16:07:10 UTC+2 schrieb >> [email protected]: >> >> >> >> Hi, >> >> >> >> I have been trying to integrate forces and convert potential to lammps >> .pot format. I used all the appropriate script but after the conversion to >> lammps the potential for angles seem unreasonable. >> >> Very high energy values. Something seems to be going wrong with >> potential_shift.pl. I would be grateful if you could share your insights >> on this. >> >> >> >> Best regards, >> >> Christianna >> >> >> >> ps. The same thing seems to be happening with Gromacs angle >> potentials. >> > >> > -- >> > 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] <javascript:>. > To post to this group, send email to [email protected] <javascript:>. > 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.
