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 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.
