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, christoph...@ <>gmail.com <http://gmail.com/> >> 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] <>> 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] <>. >> > To post to this group, send email to [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>. >> >> >> >> -- >> 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 vo...@ <>googlegroups.com <http://googlegroups.com/>. >> To post to this group, send email to vo...@ <>googlegroups.com >> <http://googlegroups.com/>. >> 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. > 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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