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 
> <alexand...@gmail.com <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 <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 
> >>> 
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> Christoph Junghans 
> Web: http://www.compphys.de 
>

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