On Thu, Apr 12, 2018 at 3:39 AM, Alexander Alexander <alexanderwie...@gmail.com> wrote: > > Hi, > > I was wondering if it is normal to have table_b1,2,3,4.xvg like the attached > figures? They are the result if BI (similar script as hexane example) over a > 500 ns nvt simulation of a single molecule. What could be the meaning of the > straight line passing from point (0,0) in table_b1.xvg for example? No they don't look normal, bonded interaction should always look like an modified U with both sides, left and right, going to infinity.
> Also, is the format of the table_bonded.xvg is "x y [error bar]"? x,y, force - see the gromacs manual for details. Christoph > Thank you. > Regards, > Alex > > On Wednesday, April 11, 2018 at 3:44:30 PM UTC-4, Christoph Junghans wrote: >> >> On Wed, Apr 11, 2018 at 12:49 PM, Alexander Alexander >> <alexand...@gmail.com> wrote: >> > >> > Hi Christoph, >> > >> > On Wednesday, April 11, 2018 at 8:22:24 AM UTC-4, Christoph Junghans >> > wrote: >> >> >> >> >> >> >> >> On Wed, Apr 11, 2018, 01:51 Alexander Alexander <alexand...@gmail.com> >> >> wrote: >> >>> >> >>> >> >>> Hi, >> >>> You mean BI over a single molecule in vacuum? >> >> >> >> >> >> Yes, or any potential, which has right equilibrium length/value. >> > >> > I decided to the BI for bonded interaction, the procedure and results >> > for >> > one of the molecule is shared in the below link, I am not sure if >> > everything >> > is fine, I would be so appreciated if you could kindly have a look and >> > give >> > any suggestion, please. >> > >> > https://drive.google.com/open?id=1hvIH9mk1LfYo5LOO1VjBAkBZx7L0q3P0 >> > >> > Also, do the settings used in the hexane or spce water example in the >> > tutorial are the real settings and parameters used in your publication? >> > or >> > these are just examples. >> Most of them are, but some got adapted a bit to be more instructive as >> tutorials. >> >> Christoph >> > >> > Thanks. >> > Regards, >> > Alex >> >> >> >> >> >>> >> >>> Instead of sd integrater can md integrator (but still in NVT ensemble) >> >>> be >> >>> used in IBI ( bonded and nonbonded or either of them) and still have >> >>> good >> >>> results? >> >> >> >> >> >> Sure as long as you are still sampling NVT you can use any integrator. >> >> However, usually sd is the more stable integrator, so I don't think >> >> that >> >> change will help with your problem. >> >> >> >> Christoph >> >> >> >>> Thanks, >> >>> Alex >> >>> >> >>> -- >> >>> 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 votca+un...@googlegroups.com. >> >>> To post to this group, send email to vo...@googlegroups.com. >> >>> 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 votca+un...@googlegroups.com. >> > To post to this group, send email to vo...@googlegroups.com. >> > 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 votca+unsubscr...@googlegroups.com. > To post to this group, send email to votca@googlegroups.com. > 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 votca+unsubscr...@googlegroups.com. To post to this group, send email to votca@googlegroups.com. Visit this group at https://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
