# [gmx-users] refcoord-scaling

Christopher Neale chris.neale at alum.utoronto.ca
Tue Mar 25 04:40:31 CET 2014

```Say you have a box with an x-side length of 3 nm and two atoms with x-dimension position restraints to: (a) x=1 nm, and (b) x=2 nm

Then let the box shrink to 99% of its previous size due to pressure coupling. The following is my understanding of  the locations to which the atoms will be restrained:

refcoord_scaling =

none:
(a) x=1 nm, and (b) x=2 nm  -- note how the restraint positions are not scaled (even though the positions of the atoms are scaled due to pressure coupling)

all:
(a) x=0.99 nm, and (b) x=1.98 nm   -- note how the atoms are now restrained to be closer together

com:
(a) x=0.985 nm, and (b) x=1.985 nm  -- note how the distance between the atoms is maintained

So you see how "none" leads to problems because the restraint reference positions are not scaled at all with the atomic positions and how "all" leads to problems because, if you restrained all Ca atoms, then you would get compression/expansion of the size of your protein as the system fluctuated in constant pressure simulations.

Chris.
________________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Chetan Mahajan <chetanvm10 at gmail.com>
Sent: 24 March 2014 23:25
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] refcoord-scaling

Thanks, Justin. I am trying to understand what is meant by 'com' option.
Following two sentences in manual seem conflicting with each other:

"*Scale* the center of mass of the reference coordinates with the scaling
matrix of the pressure coupling. The *vectors of each reference
coordinate*to the center of mass are *not
scaled*."

Doesn't scaling center of mass of reference coordinates change something
else ? reference coordinates?

Thanks

Chetan

On Mon, Mar 24, 2014 at 8:22 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 3/24/14, 9:05 PM, Chetan Mahajan wrote:
>
>> Hi Justin,
>>
>> My system is TiO2 crystal (2160 atoms position restrained) solvated by
>> 3656
>> water molecules, 1 formate anion and 1 sodium ion.  Is it true that when
>> 'all' option is used, positions of the atoms (meant to be restrained)
>> always change?
>>
>>
> Consider what position restraints are doing.  They never guarantee that
> atoms won't move; they just apply a biasing potential to disfavor movement.
>  So yes, your atoms will probably move.  The smaller the system, the larger
> the effect will likely be.  Consider also what reference coordinates are
> doing.  They define how strong the potential is (distance between current
> coordinates and reference).  If you're scaling all atoms individually
> according to the pressure coupling, the reference moves and therefore the
> atoms can also move.  For larger systems like proteins, "refcoord_scaling =
> com" is normal and stable, and "refcoord_scaling = all" is disfavored.
>  Honestly, I don't know what to expect for a very small system like yours,
> but it is likely to be affected to a greater extent.
>
> If the "all" option gives you a stable simulation that allow for proper
> equilibration, then I doubt there is any real problem.
>
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> 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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