[gmx-users] refcoord-scaling

[Chetan Mahajan]

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?

Thanks
Chetan


On Mon, Mar 24, 2014 at 7:37 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 3/24/14, 8:29 PM, Chetan Mahajan wrote:
>
>> Thanks, Mark. So is 'all' option okay when positions of each of the atoms
>> of TiO2 crystal (2160 atoms total) are restrained in space? Apparently, it
>> does not seem correct, since positions of the atoms of TiO2 crystal change
>> when 'all' option is applied. However, it does not give error as 'com'
>> option does.
>>
>>
> Is your system just a TiO2 crystal?  Is there any solvent?  If it's just a
> crystal, I see no point in restraining anything.  It is very unusual that
> the "all" option of refcoord-scaling is more stable than "com" - normally
> the opposite is true.  But that also explains why the coordinates are
> changing - the reference position of each individual atom is scaled
> according to the pressure coupling matrix, so the atoms are restrained to a
> dynamic reference, so it seems that it's not really accomplishing anything.
>
> -Justin
>
> --
> ==================================================
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> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
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> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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