2016-02-03 15:00 GMT-07:00 Chang Woon Jang <[email protected]>: > Dear Christoph, > > Thank you very much for your advice. > > Do you mean that if I use csg_inverse and then the obtained distributions > for both bond and nonboned interactions fit to target distributions, the > potentials are already extrapolated and ready to be used? Yes, the xvg file are extrapolated and ready to be used! The pot.new files are the raw data files.
> > If the simulation runs with those potentials, are the roughed forces fine? Yes! Of course there could always be the case that longer simulation expose some problems with the potentials. Christoph > > Thank you. > > Best regards, > Changwoon Jang > > On Wed, Feb 3, 2016 at 4:41 PM, Christoph Junghans <[email protected]> > wrote: >> >> 2016-02-03 13:40 GMT-07:00 Chang Woon Jang <[email protected]>: >> > Dear Votca Users, >> > >> > I am wondering about extrapolating non-bonded and bonded (bond and >> > angle) potentials from csg_inverse. >> > >> > For the bonded and non-bonded potentials obtained from Iterative >> > Boltzmann Inversion, they do not have poorly-sampled regions in >> > table_XXX.xvg files. Those non bonded potentials and forces are smooth >> > and >> > look similar to Lennard Jones potential curve. Those bonded potential >> > are >> > also smooth and U shapes. But the forces are look ugly in the side of >> > the >> > minimum. >> To clarify the *.xvg are the extrapolated and smoothed version of the >> potentials. >> For the rough version, have look at *.pot.new >> >> > >> > Questions? >> > >> > 1. If there are no poorly-sampled regions in both bonded and non-bonded >> > potentials from csg_inverse, can I just use those potentials for CG >> > simulations? >> Yes! An iteration step is already a short CG simulation. >> >> > >> > 2. Do I need to resample and extrapolate bonded FORCES if those have >> > poorly-sampled regions? >> You can always fit the potential with a smooth function or increase >> the step value to make potentials and hence forces smoother, but as in >> 1.) if it runs you should be fine. >> >> Christoph >> >> > >> > Thank you very much for your advice. >> > >> > Best regards, >> > Changwoon Jang, >> > >> > -- >> > 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. > > -- > 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.
