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 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.
