Re: [AMBER] NMR restraints not responding to 'value' flags in AMBER16 (pmemd.cuda)

From: Adrian Roitberg <>
Date: Mon, 25 Jul 2016 19:23:20 +0200

Hi Wes

did you try this in sander and also pmemd.cpu ?


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 <>
> 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:
>> 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
AMBER mailing list
Received on Mon Jul 25 2016 - 10:30:03 PDT
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