On Thu, Dec 6, 2018 at 10:48 PM Thomas Meng <[email protected]> wrote:
> Another small question is that, since the unit system in GROMACS is > different from that of LAMMPS, > possibly I need to transform the unit. The unit I use is the LAMMPS *real > *system, the energy unit is > kcal/mol, and the distance unit is Angstrom. Thus, I should change the > value of kBT in 'setting.xml' > file into 300K*0.0019872041kcal/(mol·K) = 0.5961623, and just keep the > distance units in nanometer, > is it right? > kBT should be in the same units as your potentials in LAMMPS, so if the energy unit is kcal/mol, it should be in kcal/mol. > > > And what is the unit of the bonded potential generated by the command > 'csg_boltzmann'? How do I keep > it consistant with my simulation system? > csg_boltzmann has gromacs units hard-codes (see https://github.com/votca/csg/issues/155), so you will have to manually convert energies, distances and angles as needed. Bonds are in nm and angles are in Radians. Christoph > > Meng > > 在 2018年12月7日星期五 UTC+8上午6:07:29，Christoph Junghans写道： >> >> On Thu, Dec 6, 2018 at 9:29 AM <[email protected]> wrote: >> > >> > Hi, >> > >> > I'm using VOTCA to coarse-grain a relatively simple polyether system, >> [C-C-O-C-C]n, and a super atom just represents a single monomer. After >> performing an all-atom simulation in LAMMPS, I got a trajectory file >> (trj_tail20.dump) and a final data file (nvt_300K_final.data). I wrote my >> own map and topol .xml files, and then use them to calculate the RDF of the >> system. >> > >> > What got me frustrated is that, the RDF I obtained using csg_stat >> (figure AA.png) seems to be questionable. Because if I use LAMMPS to >> generate the RDF of the central O atom using the final data file, I got a >> different result (AA-LAMMPS.png). And the most strange thing is that if I >> use OVITO to analyze the CG configuration I converted using the csg_map >> command, I got a similar result compared to that of lammps simulation >> (AA-OVITO.png). >> > >> > Because the RDF is a quite important intermediate process file, so I >> wonder what resulted in the above difference? And could I trust the one >> generated through VOTCA? >> >> csg_stat has been tested over years, so I don't think there is a >> problem in the code. >> But I saw your topol.xml has a <bond> section, which in VOTCA >> generates a bunch of RDF exclusions, i.e. pairs in a bond aren't >> considered for the RDF calculation. You can see that running: >> $ csg_dump --top topol.xml --excl >> >> So if you don't want that just delete that section. >> >> Also in the development version of VOTCA you can use LAMMPS' data >> files as topology input directly. >> >> Christoph >> >> > >> > Meng >> > >> > P.S. >> > The command I used to generate RDF is "csg_stat --top topol.xml --trj >> trj.dump --cg cg.xml --options settings.xml" >> > >> > -- >> > 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. > -- 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.
