[gmx-users] Harmonic restraint in FEP

[Justin Lemkul]

On 7/13/16 5:36 PM, Alexander Alexander wrote:
> Thanks Justin for your response.
> I have already seen read the manual and every thing is clear for me for the
> "coul-lambdas" and "vdW-lambdas"and available examples. As far as I
> understand in FEP, when we want to get rid if something gradually for
> example vdW or charge, then we go from 0.0 ..... to 1.0 meaning in 0.0 they
> are present but in 1.0 they are absent which I think is th same for all the
> XXX-lambdas.

This is not correct in the general sense.  It depends entirely upon how you 
define the transformation and/or A-B transitions in the bonded terms. For instance:

couple-lambda0 = none
couple-lambda1 = vdw-q

does the exact *opposite* of what you describe above when moving from lambda = 0 
to lambda = 1.  The "direction" of the transformation is up to the user to define.

> So, when I want to turn on or apply or have harmonic restrain then the
> restraint-lambdas
> should goes from 1.0 to 0.0, however it is in contradict with some examples
> in which the harmonic restraint is going to be applied and that confuse me
> a bit.
>
> In summary, I want to apply gradually harmonic restraints, so,
> reasonably, restraint-lambdas
> = 1.0 0.8 0.6 0.4 ... 0.0 ?
>

Similarly, this depends entirely on what you set using pull-coord1-k and 
pull-coord1-kB.  If you set:

pull-coord1-k = 0.0
pull-coord1-kB = 1000.0

you can turn on the restraint with restraint-lambdas = 0.0 0.2 ... 1.0

or you can turn them on with

pull-coord1-k = 1000.0
pull-coord1-kB = 0.0

and restraint-lambdas = 1.0 0.8 ... 0.0

Whatever makes the most sense to you.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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