.Adrian
We have finished running the Ca2+ test case using pmemd.mpi and sander.mpi.
Both are showing the same behavior. E.g. the value1 and value2 flags seem
to have no effect, but directly setting rk1 and rk2 works appropriately.
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
> >>
> > _______________________________________________
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>
> --
> 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 - 16:30:02 PDT
