2016-08-15 12:49 GMT-06:00 Chang Woon Jang <[email protected]>: > Dear Christoph, > > I have iterated the interactions only not converged RDFs from step_300. > Now, it reaches step_400. The new RDFs do not seem to converge the target > RDFs. > > Is this because of so many non-bonded potentials? In my system, there are 28 > non-bonded interactions from 7 bead types. > > Do I just use the best matched potentials? Yes, but remember to use potentials, which are all from the same iteration step.
Christoph > > Best regards, > Changwoon Jang > > > > On Mon, Aug 8, 2016 at 6:19 PM, Christoph Junghans <[email protected]> > wrote: >> >> 2016-08-08 14:24 GMT-06:00 Chang Woon Jang <[email protected]>: >> > Dear Christoph, >> > >> > I have followed the option 1) Stop after 300 steps, change your >> > settings.xml (i.e. set do_potential to "0" for converged potentials) and >> > go >> > on in the same directory structure.) >> > >> > When I set do_potential to "0" for few of interactions, for example A-B, >> > the >> > radial distributions are still moving. The attachment is the plot for >> > A-B >> > RDFs from step_300 step and step_304. >> > >> > Is this correct for "0" do_potential RDFs still changing? If it is >> > correct, >> > what is the influence of "0 do_potential" in settings.xml? >> Yes, the RDFs can change if other interactions in the system change, >> it just means your RDFs are inter-dependent, which is quite common. >> >> Christoph >> > >> > Thank you. >> > >> > Best regards, >> > Changwoon Jang >> > >> > >> > On Mon, Aug 8, 2016 at 1:55 PM, Christoph Junghans <[email protected]> >> > wrote: >> >> >> >> 2016-08-08 10:26 GMT-06:00 Chang Woon Jang <[email protected]>: >> >> > Dear Christoph, >> >> > >> >> > Thank you for your comments. If I iterate only not converged >> >> > potentials, >> >> > can I use the potentials converged over 300 steps? >> >> Yes! >> >> >> >> > >> >> > >> >> > Do I need to just modify the settings.xml file to iterate only not >> >> > converged RDFs? Do I just remove all converged RDFs, >> >> > <non-bonded>....</non-bonded>? >> >> Option 1a.) Stop after 300 steps, change your settings.xml (i.e. set >> >> do_potential to "0" for converged potentials) and go on in the same >> >> directory structure. >> >> Option 1b.) Copy <NAME>.pot.cur from step 300 to a new directory >> >> structure under the name <NAME>.pot.in and don't iterate them by >> >> setting do_potential to "0". >> >> Option 2.) Copy table_XXX.xvg to a new directory structure and remove >> >> the <non-bonded>....</non-bonded> for the or converged potentials. >> >> >> >> Christoph >> >> > >> >> > >> >> > Thank you very much. >> >> > >> >> > Best regards, >> >> > Changwoon Jang >> >> > >> >> > >> >> > >> >> > On Mon, Aug 8, 2016 at 12:18 PM, Christoph Junghans >> >> > <[email protected]> >> >> > wrote: >> >> >> >> >> >> 2016-08-08 9:26 GMT-06:00 Chang Woon Jang <[email protected]>: >> >> >> > Dear Votca Users, >> >> >> > >> >> >> > I have run IBI for the system with 7 types of beads. Total 28 >> >> >> > non-bonded >> >> >> > interactions. >> >> >> > >> >> >> > I have reached 500 steps. Each step runs about 8 ns (8000000 >> >> >> > iterations). >> >> >> > Few of RDFs do not converge to the target RDFs. I keep running the >> >> >> > IBI >> >> >> > but >> >> >> > the RDFs do not seem to be converged because the first peaks of >> >> >> > new >> >> >> > RDFs >> >> >> > do >> >> >> > not come down to the target peaks after 300 steps. >> >> >> > >> >> >> > Do I need to change some settings or do something else? Any >> >> >> > comments >> >> >> > are >> >> >> > appreciated. >> >> >> This is really system-depend! You could try to just iterate the >> >> >> interactions of the not converged RDFs starting from the potentials >> >> >> from step 300. >> >> >> >> >> >> Christoph >> >> >> >> >> >> >> >> >> > >> >> >> > >> >> >> > Thank you. >> >> >> > >> >> >> > 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. >> >> > >> >> > >> >> > >> >> > >> >> > -- >> >> > Best regards, >> >> > Changwoon Jang, >> >> > >> >> > Postdoctoral Research Fellow >> >> > Department of Chemical & Biological Engineering, Drexel University >> >> > 3141 Chestnut Street, Philadelphia, PA 19104 >> >> > >> >> > Voice: (662) 617-2267 >> >> > E-mail: [email protected] >> >> > >> >> > -- >> >> > 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. >> > >> > >> > >> > >> > -- >> > Best regards, >> > Changwoon Jang, >> > >> > Postdoctoral Research Fellow >> > Department of Chemical & Biological Engineering, Drexel University >> > 3141 Chestnut Street, Philadelphia, PA 19104 >> > >> > Voice: (662) 617-2267 >> > E-mail: [email protected] >> > >> > -- >> > 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. > > > > > -- > Best regards, > Changwoon Jang, > > Postdoctoral Research Fellow > Department of Chemical & Biological Engineering, Drexel University > 3141 Chestnut Street, Philadelphia, PA 19104 > > Voice: (662) 617-2267 > E-mail: [email protected] > > -- > 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.
