2015-05-28 21:56 GMT-06:00 Tonalli Rodríguez <[email protected]>: > Ok. I have included the pre-simulation in the simplex_water-bulk tutorial > and it's running now, but I had to run the atomistic case in order to get > the rdf in the range (0,1). Could you help me to understand why is necessary > a lower limit less than 0.24? Well, let me emphasize that the pre-simulation feature is only implemented for Gromacs, but not for the LAMMPS or any other simulation back-end.
The lower limit comes from two facts: 1.) The Boltzmann inverted potential for g(r)=0 is undefined as log(0)=-inf. 2.) The Boltzmann update is also undefined for g(r)=0 and even worse for values close to 0 (which are 0 in some iterations and else not) the update systematically goes in one direction. VOTCA has some magic tricks to work around these issues, but it is much cleaner to let the user decide where to calculate the update. In addition, in the case of LAMMPS there is a table_begin option, which tells VOTCA how far from min the table should be extrapolated. > I have attached the corresponding tutorials > with lammps as the MD package. Once again, thank you for your immediate Is there something I need to look at or do you just wanted to share them? Would it make sense to add them to our csg-tutorial repository? > response. By the way, is it possible to write the parameters to a file that > can be read it by lammps? For example, the "spce.in" could be Writing the parameters to spce.in could be done, but remember that VOTCA supports basically any functional form for the potential that gnuplot can parse. This is a much bigger set of potentials than what LAMMPS and especially GROMACS supports and hence taking the detour over tabulated potential makes sense. Christoph > > # begin file "spce.in" > units lj > atom_style atomic > > read_data spce.data > > velocity all create 2.49 87287 > > pair_style lj/cut 1.0 > include forcefield.CG_CG > > timestep 0.001 > fix 1 all nve > fix 2 all langevin 2.49 2.49 0.2 545454 > > dump 1 all atom 1000 traj.dump > > thermo 50 > run 1000 > # end file "spce.in" > > # begin file "forcefield.CG_CG" > pair_coeff 1 1 0.65 0.31 > # end file "forcefield.CG_CG" > > Of course, using votca. > > Tonalli > > -- > 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 http://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 http://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
