what do you mean by "before autoimage"? autoimage is a cpptraj command, but
it sounds like you are talking about what happens in the MD run.
do you have iwrap=1 in your simulation?
On Thu, Mar 18, 2021 at 12:15 AM Ming Tang <m21.tang.qut.edu.au> wrote:
> Dear Carlos and David,
>
> Thank you very much for your guidance. Yes, I found that a positive rk2
> does the right thing and the problem lies in how the system calculates the
> distance between two IGRs. I found out that the system calculates the
> distance based on the coordinate before autoimage, and therefore the small
> molecules do not get close in the trajectory before the autoimage process.
> I guess this comes from the periodic boundary condition setting.
>
> Is there a way to fix this?
>
> Many thanks,
> Ming
> ________________________________
> From: Carlos Simmerling <carlos.simmerling.gmail.com>
> Sent: Tuesday, 16 March 2021 11:41 PM
> To: AMBER Mailing List <amber.ambermd.org>
> Subject: Re: [AMBER] Apply Lennar-Jones potential between small molecules
>
> On Tue, Mar 16, 2021 at 8:56 AM David A Case <david.case.rutgers.edu>
> wrote:
>
> > On Tue, Mar 16, 2021, Carlos Simmerling wrote:
> >
> > >yes negative rk gives an inverted parabola, so it is repulsive if it is
> > >outside the flat region.
> >
> > I'm a little confused here, and would recommend careful testing if you
> are
> > setting rk2 to a negative number. I've not done that but it *sounds*
> > dangerous. Probably a good idea to numerically plot the function vs.
> > distance, and make sure you are getting the behavior you want.
> >
> >
> Dave is right, this can be really dangerous since it goes to infinitely
> negative energies. I've used it and technically it does work, but it's
> probably much safer to use other options. I should have been more careful
> in giving caution along with my reply!
>
> re-reading the original question, a negative rk2 will make them ATTRACTIVE
> below r2, and it doesn't sound like this is what you want. *For repulsive
> interaction below r2 you want a positive rk2.*
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Received on Thu Mar 18 2021 - 04:00:02 PDT
