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.
