I would not think about what happens after autoimage- that's not what is
going on in your simulation and the restraints will only be applied to what
happens during MD.
focus on the input structure that you give to sander or pmemd, and whether
you use imaging during MD or not. also on how you set up the pairs and
distances for the restraints.
can you simplify the problem to a single restraint that you think isn't
working, and explain what your restraint is, the initial coordinates for
that pair, and why you think it isn't working during MD?
On Thu, Mar 18, 2021 at 10:53 AM Ming Tang <m21.tang.qut.edu.au> wrote:
> Yes. I tried both iwrap=0 and 1, and the distance is same and not real
> (not equal to the distance after the cpptraj autoimage process)
> ________________________________
> From: Carlos Simmerling <carlos.simmerling.gmail.com>
> Sent: Thursday, 18 March 2021 8:35 PM
> To: AMBER Mailing List <amber.ambermd.org>
> Subject: Re: [AMBER] Apply Lennar-Jones potential between small molecules
>
> 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 - 08:30:02 PDT
