On Tue, Nov 20, 2018 at 2:04 AM Lee <[email protected]> wrote: > > I have another question. If my units command is real in lammps which the > units of distance and energy are angstroms and Kcal/mole respectively, what > shoud I change in the setting file in order to get the potential table with > right units? Now, the bond and angle potential of the CG system are much > lower than the corresponding atomic system.
Usually VOTCA calculated things in Gromacs units (so nm, kJ/mol etc.), but if you only calculate RDFs you don't need to change anything as input and output are both in nm and hence there is no scaling involved. So this will work for angstroms as well. Additionally, you need to make sure that kBT is in the right unit in the settings file. Christoph > Thanks a lot. > > 在 2018年11月20日星期二 UTC+8上午5:52:29，Christoph Junghans写道： >> >> On Mon, Nov 19, 2018 at 8:51 AM Christoph Junghans <[email protected]> wrote: >> > >> > On Sun, Nov 18, 2018 at 8:31 PM Lee <[email protected]> wrote: >> > > >> > > For the dynamic simulations finished with lammps, should I set the >> > > exclusions? If excluding non-bonded interactions between atoms that are >> > > no further than 3 bonds away, does it need to excluding these atoms when >> > > statistical target rdf distributon? >> > > >> > Yes, for LAMMPS you will most likely need to create rdf exclusion manually. >> > >> > You can check, what exclusion VOTCA see by running: >> > $ csg_dump --top <your_topology_file> --excl >> > >> > For advanced topology handling see, section 3.3 of the manual, >> > http://doc.votca.org/manual.pdf >> Also Joshua might be able to say something about the new LAMMPS >> topology reader in csg and how exclusions are incorporated there. >> >> Christoph >> > >> > Christoph >> > > -- >> > > 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 >> >> >> >> -- >> 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.
