Re: [AMBER] defining reaction coordinate for umbrella sampling

From: Jason Swails <>
Date: Sun, 1 Jun 2014 22:09:50 -0400

On Sun, Jun 1, 2014 at 9:12 PM, Jorgen Simonsen <> wrote:

> Hi ,
> I am trying to perform a QM/MM reaction and would like to sampling along a
> reaction coordinate using umbrella sampling.
> My reaction is a SN2 attack where atom 10, an oxygen of hydroxide, is
> attack a carbon atom number 12, which is bound to a leaving group with atom
> 14 another oxygen.
> I have set the system up like this:
> variable
> type=LCOD
> i = (10,12,14)
> r = (1.0,-1.0)
> anchor_position = 3.0
> anchor_strength = 10.0
> end variable

​Not many people use the NCSU codes these days as far as I know (especially
not those that respond regularly to questions on this list). The manual
along with trial and error is your best bet for seeing what works. I'll
try to give some advice, but you will likely find more support for this
functionality as it is implemented in the NMR restraint section (see
chapter 23 of the Amber 14 manual).

That said, I don't know that you can define a LCOD restraint with only 3
atoms. The manual suggests that the atoms need to be specified in pairs
(so you would need i = (10, 12, 12, 14) in your case). I know you need
either 4 (for 2 distances), 6 (for 3 distances), or 8 (for 4 distances)
atoms specified for the LCOD code in the NMR restraint section. I suspect
the NCSU codes have the same requirement.

> I do not understand where I would defined maximum distance for my reaction
> also it is not clear to me how you specify the intervals being sampling
> along the reaction coordinate e.g. I would like to sample with a step size
> of 0.2 Å for this reaction coordinate but after 6 Å I do not want to apply
> any force for the reaction coordinate. I am using amber12 - thanks for any
> suggestions.

​I don't know if I understand what you want. With umbrella sampling, you
have a single harmonic potential centered at a single point. That
potential never moves. And you simulate numerous windows along your
reaction coordinate. So if your coordinate goes form 3 to 6 angstroms,
then you should run a simulation with windows in which the umbrellas
centered between 3 and 6 angstroms at 0.2 Å intervals (3.0, 3.2, 3.4, 3.6,
..., 6.0 Å).

There is no way to turn "off" the harmonic potential after a certain
distance (there is no continuous derivative -- and therefore no continuous
force -- for such a potential!). And this is not steered MD in which the
center of the potential moves from the beginning to the end, "driving" the
reaction forward (or backward). The potential is simply augmented by a
single, 3-D quadratic potential.​


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Sun Jun 01 2014 - 19:30:02 PDT
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