Hi, Thank you very much, that makes more sense. So if I have understood correctly, when I have a LAMMPS trajectory with forces, I compute forces with csg_fmatch, I integrate forces with csg_call integrate. In case I have used units real I have to scale by 0.2390006. Does this scaling have to happen for all interactions? And does it have to go in the settings.xml within <scale></scale> section? And then I just need to remove shifting. Do I remove only for angles or for every interaction ?
When I have GROMACS trajectory I also have a problem with the angle potentials created after the convert potential. What kind of scaling or what I need to do in this case. Thank you in advance! 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 > > <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] <javascript:>> 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 > > <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 <http://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] <javascript:>. > > To post to this group, send email to [email protected] <javascript:>. > > Visit this group at https://groups.google.com/group/votca > > <https://groups.google.com/group/votca>. > > For more options, visit https://groups.google.com/d/optout > > <https://groups.google.com/d/optout>. > > > > -- > Christoph Junghans > Web: http://www.compphys.de <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] > <mailto:[email protected]>. > To post to this group, send email to [email protected] > <mailto:[email protected]>. > Visit this group at https://groups.google.com/group/votca > <https://groups.google.com/group/votca>. > For more options, visit https://groups.google.com/d/optout > <https://groups.google.com/d/optout>. -- You received this message because you are subscribed to the Google Groups "votca" group. 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