2015-12-23 8:34 GMT-07:00 Chang Woon Jang <[email protected]>: > Dear Christoph, > > Thank you for your kind answers. I know that Lammps can handle nm and > KJ/mol dependent on the unit setting in Lammps. > > I have one more question about csg_fmatch. Does this command also use KJ/mol > and KJ/mol-nm because I analysed Gromacs trajectory? csg_fmatch reads distances and force for the trajectory and write the output in the same units. Hence when using a Gromacs trajectory it reads nm and kJ/mol/nm and write in the same units.
Christoph > > Thank you. > > Best regards, > Changwoon Jang > > On Tue, Dec 22, 2015 at 7:14 PM, Christoph Junghans <[email protected]> > wrote: >> >> 2015-12-22 16:53 GMT-07:00 Chang Woon Jang <[email protected]>: >> > Dear Christoph, >> > >> > I mean the file written by csg_boltzmann with Tab command. If >> > csg_boltzmann used GROMACS units, I think the second column (energy) in >> > KJ/mol, and the third column (force) in KJ/mol-nm. Am I right? >> Correct! (Assuming your input was in nm). >> >> > >> > In lammps I will use, the energy should be Kcal/mol and the force should >> > be >> > Kcal/mol-Angstrom. >> And again lammps can use nm and KJ/mol, too. >> >> Christoph >> >> > >> > Therefore, I would like to make sure that the file units from >> > csg_boltzmann >> > Tab use KJ/mol and KJ/mol-nm. >> > >> > If I am wrong, please correct me. >> > >> > Thank you. >> > >> > Best regards, >> > Changwoon Jang >> > >> > >> > On Tue, Dec 22, 2015 at 6:30 PM, Christoph Junghans <[email protected]> >> > wrote: >> >> >> >> 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. >> > >> > >> > -- >> > 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. 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