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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Received on Mon Jul 25 2016 - 14:30:03 PDT
