Not yet. The system is rather large. We will try running the small Ca ion
test system with all three and see what happens.
-Wes
On Mon, Jul 25, 2016 at 10:23 AM, Adrian Roitberg <roitberg.ufl.edu> wrote:
> Hi Wes
>
> did you try this in sander and also pmemd.cpu ?
>
> adrian
>
>
>
> On 7/25/16 7:21 PM, Wesley Michael Botello-Smith wrote:
> > Yes, I read the listed link. In fact it is that tutorial (along with the
> > simulated annealing example in the AMBER manual nmr restraint section)
> that
> > I was following in order to modify my original input file to perform the
> > force constant scaling.
> > You can see, if you look at my original email, that I am doing
> essentially
> > the same thing, excepting that I am not scaling temperature (no TAUP
> flag).
> >
> > Effectively, the 'value1' and 'value2' flags are scaling the force
> > constants rk1 and rk2, according to the tutorial you listed as well as
> the
> > AMBER16 manual. This is done linearly across the range of timesteps
> defined
> > by 'istep1' and 'istep2'
> > The problem is, that this is not actually happening. This is evident
> because
> > 1) The value of the 'RESTRAINT' term in the energy printouts does not
> scale
> > down to zero as it should when value2=0
> > and
> > 2) The distance between the two atoms being restrained does not increase
> > significantly like it does if rk1 and rk2 are set to 0.
> > So I'm trying to figure out why the 'REST' option is, apparently, having
> no
> > effect whatsoever.
> >
> > We are constructing a simple example of 2 Ca2+ ions in a small water box
> to
> > see if we can replicate this problem on a smaller system.
> > -Wes
> >
> > On Mon, Jul 25, 2016 at 12:34 AM, ankita mehta <mehtaroadies.gmail.com>
> > wrote:
> >
> >> And if u understand you can reduce the restraints in one simulation
> >> run....however first u should understand how this works....
> >> On Jul 24, 2016 11:48 PM, wrote:
> >>
> >> Can u pls read the following:
> >>
> >> Finally, we vary the weight of the restraints using type='REST'. This
> >> affects the force constants (rk2 and rk3) we had input in the restraint
> >> file, and the effective force constant is multiplied by the weight we
> give
> >> the restraints. We will gradually increase the weight from 0.1 to 1
> between
> >> step 0 and step 3000. Starting with a smaller weight on the restraints
> >> ensures that large violations in the initial structure do not cause the
> >> system to blow up, and that the structure will quickly adjust in the
> >> beginnning of the simulation to get rid of the really high violations.
> For
> >> the rest of the run (step 3001 to 20000), we will keep the weight of the
> >> restraints at 1. Following that, we end the weight change section with
> >> type='END'.
> >>
> >> I took this from the following link:
> >>
> >>
> www.uni-koeln.de/themen/chemie/software/amber7/tutorial/dna_NMR/nmr_dna_tutorial.htm
> >>
> >> It will make u understand the things...
> >> I hope this helps....
> >> _______________________________________________
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> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
> --
> Dr. Adrian E. Roitberg
> University of Florida Research Foundation Professor.
> Department of Chemistry
> University of Florida
> roitberg.ufl.edu
> 352-392-6972
>
>
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Received on Mon Jul 25 2016 - 11:00:02 PDT
