[gmx-users] SPC Water Bond Lengths

[Justin Lemkul]

On 5/3/14, 6:34 PM, David Ackerman wrote:
> Hello,
>
> I had a question regarding SPC water. I know that SPC water is rigid with
> constrained bond lengths. However, I have noticed in my simulations that
> the OH bond lengths and H-H distances can vary somewhat significantly. For
> instance, I have run simulations containing ~140000 SPC waters, and the
> average OH bond length is around ~0.79 Angstroms, with a max of 1 and a
> minimum of nearly 0. Also, dppc128.pdb from
> http://people.ucalgary.ca/~tieleman/download.html, which utilized SPC
> waters, also has an average OH bond length of ~0.79 Angstroms. In both
> cases, I see a distribution in bond lengths that is very high near 1
> Angstrom, and dies off as it approaches 0.
>
> I was wondering if this is expected. Assuming the water is rigid, should
> the bond lengths remain more fixed than what I am seeing?
>
> I apologize if this is an ignorant question, but aside from seeing that SPC
> water is supposed to be rigid, I have seen no mention of bond length
> distributions.
>

There should be no distribution.  The bond lengths should be fixed.  How are you 
measuring these values to give rise to these distributions?  If an O-H bond 
length actually approached zero, the constraint algorithm would fail and the 
simulation would die.  In fact, even a very small deviation from the constraint 
length would trigger obvious warnings in the .log or stderr output.

-Justin

-- 
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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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