.David
I can verify that setting both value1=0 and value2=0 makes a significant
change. However,
if I set value1=1 and value2=0, there is no longer a significant change.
This would indicate that the restraints are not being ramped down correctly.
You can verify this in the output files I am sending.
-> gcg.dip.o.save (original)
-> gcg.dip.o (scales restraints using value1=1 and value2=0)
-> gcg.dip.o.noREST (turn off restraints using value1=0 and value2=0)
you can see that in the 'noREST' output file the 'RESTRAINT' term on the
energies is significantly lower than in the .save file, however, when
value=1 and value2=0, there is no significant change (e.g. 'RESTRAINT' term
differs only in the last one or two digits)
-Wes
On Tue, Jul 26, 2016 at 7:00 AM, ankita mehta <mehtaroadies.gmail.com>
wrote:
> Yesterday you sent me mail
> It got deleted..
> Pls resend...
>
> ---------- Forwarded message ----------
> From: *Wesley Michael Botello-Smith* <wmsmith.uci.edu>
> Date: Tuesday, July 26, 2016
> Subject: [AMBER] NMR restraints not responding to 'value' flags in AMBER16
> (pmemd.cuda)
> To: AMBER Mailing List <amber.ambermd.org>
>
>
> I just noticed a typo in my email (mdin files are correct) it should read
> value1=1.0 to value2=0.0, NOT value1=1.0 to value2=2.0.
>
> On Mon, Jul 25, 2016 at 2:25 PM, Wesley Michael Botello-Smith <
> wmsmith.uci.edu> wrote:
>
> > Here are the relevant files for a smaller test system, 2 Ca2+ ions in a
> 10
> > Å water box with Cl- counter ions.
> >
> > step3 = starting point obtained from charmm web gui
> > step4.0 = minimization (positional restraints only)
> > step4.1 = solvent equilibration (positional restraints plus nmr distance
> > restraints)
> > step4.2 = equilibration with nmr distance restraints
> > ---
> > step4.3 = ramp down nmr distance restraint from value=1.0 to value=2.0
> > over 1ns
> >
> > step4.4 (starts from same point as step 4.3, but different setup) = turn
> > nmr force constants to zero (rk1=0, rk2=0 in .rest file)
> > ---
> >
> > The restraint is very stiff (rk1=50, rk2=50), so it keeps the ions held
> in
> > place quite well.
> >
> > As is evident from the .out files and the .distout files, step4.3 shows
> no
> > apparent change in separation across its duration, whereas in step4.4,
> the
> > Ca ions fly apart rapidly.
> >
> > hopefully this is enough to replicate the error.
> >
> > This simulation was run using the latest (updated) version of AMBER16 as
> > of July 22, using pmemd.mpi for minimization and pmemd.cuda for all
> > equilibration steps.
> >
> > On Mon, Jul 25, 2016 at 10:52 AM, Wesley Michael Botello-Smith <
> > wmsmith.uci.edu> wrote:
> >
> >> 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....
> >>> >> _______________________________________________
> >>> >> AMBER mailing list
> >>> >> 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
> >>>
> >>>
> >>> _______________________________________________
> >>> AMBER mailing list
> >>> AMBER.ambermd.org
> >>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>
> >>
> >>
> >
> _______________________________________________
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>
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- application/octet-stream attachment: gcg.dip.o
Received on Tue Jul 26 2016 - 11:30:02 PDT
