Hi, I didn't see that your original trajectory was done with LAMMPS. Sorry. So, you do not have to concert the energies then.
Best Christoph CHRISTINA-ANNA GATSIOU <[email protected]> schrieb am Do., 25. Apr. 2019, 17:07: > I am just confused cause you suggested the conversion to kcal/mol even > though my initial trajectory is LAMMPS. I have a lammps trajectory (real > units) and I want to generate lammps .pot files for lammps (real units). I > didn't understand why I need to do the conversion. > Best regards, > Christianna > > On 25 Apr 2019, at 4:37 PM, [email protected] wrote: > > 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] 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]. >> 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. > > > -- > 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. 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