Am 2. Januar 2012 15:18 schrieb Javier Ramos <[email protected]>: > Thank you very much for your answers. > > Concerning the second question. I understood from the Espresso manual > that the force is, as you say, U'(r)/r being the r the distance > between two beads in the case of tabulated non-bonded potentials. > However, in the case of tabulated angle potentials I am not be able to > understand the meaning of r. Which is the r that I have to use?. Or > the second column is just U'(theta)/theta in radians? I am not sure, see here: <http://git.savannah.gnu.org/cgit/espressomd.git/tree/src/tab.h#n628>
I guess, that is a good question for the espresso mailing list: <https://savannah.nongnu.org/mail/?group=espressomd> Christoph > > I hope do not disturb you with these questions and again thank you > very much for your kindly help and patience. > > Best regards, > Javi > > On 2 ene, 20:43, Christoph Junghans <[email protected]> wrote: >> Am 2. Januar 2012 07:19 schrieb Javier Ramos <[email protected]>:> Happy new >> year everybody, >> >> > Christoph thanks for your reply, it was very useful for me. >> >> > I have a couple of new questions. In the propane tutorial, there is a >> > folder for ibi_espresso, in which the table_a1.tab file is located. >> >> > By comparing this file with the table_a1.xvg file in the ibi folder, >> > it rises two new questions. >> >> > i) The third column in table_a1.tab is the same potential than in the >> > second column (in kJ/mol) of the table_a1.xvg file. Do should not the >> > third column in table_a1.tab be in kT (reduced) units? >> >> Yes, but in that tutorial we choose sigma to be 1nm and epsilon to be 1 >> kJ/mol. >> >> > ii) I am not able to reproduce the second column of table_a1.tab from >> > direct differentiation of the third column respect to the first one >> > after appropriated change of units? >> >> Well, Espresso is special. The second column is the value of the Force >> (U'(r)/r) and not just U'(r). Mind the difference. >> >> > An additional request, may you provide the files to perform the >> > propane MD atomistic simulation in future versions of VOTCA tutorials >> > as you provide the atomistic simulation files for the hexane example? >> >> I have to look if we find that data. >> >> Christoph >> >> >> >> >> >> > Best regards, >> > Javi >> >> > On 20 dic 2011, 16:50, Christoph Junghans <[email protected]> wrote: >> >> Am 20. Dezember 2011 03:49 schrieb Javier Ramos <[email protected]>:> I >> >> am trying to perform the simulation with the propane example in the >> >> > tutorials. I have two questions concerning the table_a1.xvg file >> >> > containing the tabulated potential. >> >> >> > i) The second column contains the potential, I am assuming that the >> >> > units are in kJ/mol (gromacs units), is that correct? >> >> >> Yes, correct! >> >> >> > ii) The third column (force) is zero in the whole angle interval. >> >> > Why? >> >> >> Gromacs calculates the forces internally if all forces are zero. >> >> In case you give forces, it will warn you if the force deviate too >> >> much from the calculates ones. >> >> >> A side note: VOTCA (csg_boltzmann,csg_stat) calculates in rad, while >> >> gromacs uses degree. >> >> >> Christoph >> >> >> > Best regards, >> >> > Javi >> >> >> > -- >> >> > You received this message because you are subscribed to the Google >> >> > Groups "votca" group. >> >> > To post to this group, send email to [email protected]. >> >> > To unsubscribe from this group, send email to >> >> > [email protected]. >> >> > For more options, visit this group >> >> > athttp://groups.google.com/group/votca?hl=en. >> >> >> -- >> >> Christoph Junghans >> >> Web:http://www.compphys.de >> >> > -- >> > You received this message because you are subscribed to the Google Groups >> > "votca" group. >> > To post to this group, send email to [email protected]. >> > To unsubscribe from this group, send email to >> > [email protected]. >> > For more options, visit this group >> > athttp://groups.google.com/group/votca?hl=en. >> >> -- >> Christoph Junghans >> Web:http://www.compphys.de > > -- > You received this message because you are subscribed to the Google Groups > "votca" group. > To post to this group, send email to [email protected]. > To unsubscribe from this group, send email to > [email protected]. > For more options, visit this group at > http://groups.google.com/group/votca?hl=en. > -- Christoph Junghans Web: http://www.compphys.de -- You received this message because you are subscribed to the Google Groups "votca" group. To post to this group, send email to [email protected]. To unsubscribe from this group, send email to [email protected]. For more options, visit this group at http://groups.google.com/group/votca?hl=en.
