[gmx-users] SPC Water Bond Lengths

[Justin Lemkul]

On 5/3/14, 7:00 PM, David Ackerman wrote:
> 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?
>

It is, but I can't reproduce your findings.  Running spc216.gro through g_bond 
produces the expected output - an extremely narrow distribution that spans the 
range of 0.099 - 0.101 nm (avg ± stdev is 1.0000 ± 0.0004).  Simply visualizing 
spc216.gro confirms there are no weird geometries, though your numbers would 
suggest something should be obviously wrong.

I suspect something in your calculation has gone wrong.

-Justin

> -David
>
>
> 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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-- 
==================================================

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

==================================================