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? 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.
