[gmx-users] refcoord-scaling

[Chetan Mahajan]

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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