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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--
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 - 10:30:03 PDT
