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? Also, is the format of the table_bonded.xvg is "x y [error bar]"? 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 > <[email protected] <javascript:>> 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 <[email protected]> > >> 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 [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] <javascript:>. > > To post to this group, send email to [email protected] > <javascript:>. > > 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.
