[gmx-users] SPC Water Bond Lengths

[David Ackerman]

You are correct, I had a mistake in my code. Thank you for your help.

-David


On Sat, May 3, 2014 at 7:08 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>
> ==================================================
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