[gmx-users] SPC Water Bond Lengths

David Ackerman da294 at cornell.edu
Sun May 4 01:00:49 CEST 2014

I calculated the bond lengths by printing out the x,y,z coordinates of the
oxygens and hydrogens and calculating the distances between them.
Similarly, for dppc128.pdb, I calculated the distances based on the x,y,z
coordinates of the oxygens and hydrogens. I also see a similar distribution
to what I mentioned when doing the same calculation for spc216.gro.

Is the distance between oxygens and hydrogens not the correct way to
estimate bond length?


On Sat, May 3, 2014 at 6:39 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

> 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
> --
> ==================================================
> 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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