2015-12-22 15:56 GMT-07:00 Chang Woon Jang <[email protected]>: > Dear Christoph, > > Thank you, Christoph. I have one more question. I ran an atomistic > simulation in GROMACS. > > Are the units written in the file KJ/mol and KJ/mol-nm for energy and force, > respectively? Yes & no, csg_boltzmann uses Gromacs units. While csg_inverse uses nm and the rest depends on what you use for k_B*T in the settings file.
However, lammps can do simulation in nm as well, see the spce/ibi_lammps example: <https://github.com/votca/csg-tutorials/tree/master/spce/ibi_lammps> Christoph > > I need to convert and format the energy and force for Lammps simulation. > > Thank you. > > Best regards, > Changwoon Jang > > > On Tue, Dec 22, 2015 at 5:44 PM, Christoph Junghans <[email protected]> > wrote: >> >> 2015-12-22 15:04 GMT-07:00 Chang Woon Jang <[email protected]>: >> > Dear Votca Users, >> > >> > I have used csg_boltzmann with "tab" command to write the >> > Boltzmann-inverted potential. >> > >> > It gives three columns. In the manual, the format of the file is >> > described >> > in sec 3.6. It states that "Those tables generally have the format >> > >> > x y [error] flag >> > >> > where x is input quantity (e.g. radius, angle), y is the computed >> > quantity >> > (e.g. a potential) and [error] is an optional error for y." >> > >> > However, I do not believe that the third column is error because when I >> > draw >> > the third column as a function of radius (the first column) is much much >> > bigger than the second column. Also, there is no flag. >> > >> > Is this still correct format of Boltzmann-inverted potential file from >> > Tab >> > command of csg_boltzmann as described in Votca Manual? >> csg_boltzmann uses a different format for table than csg_inverse (sec. >> 3.6). >> csg_boltzmann writes the force in 3rd column. >> >> Cheers, >> >> Christoph >> > >> > I attached the figure for you. >> > >> > -- >> > Best regards, >> > Changwoon Jang, >> > >> > -- >> > 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. -- 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.
