[gmx-users] Minimum periodic distance

[Tsjerk Wassenaar]

Hi Kavya,

There is no way to correct for such things afterwards. But I would
guess it's not much of a problem in your case. If a situation with a
short distance is only transient, it is unlikely to affect the
simulation. On the other hand, you may have secondary, indirect
effects due to water ordering. Whether that is problematic in your
case is something you'll have to assess yourself.

Cheers,

Tsjerk

On Mon, May 30, 2011 at 12:24 PM, Kavyashree M <hmkvsri at gmail.com> wrote:
> Hello Sir,
>
> The difference between the rcolumb (1.4nm) and minimum image distance
> that was obtained between two hydrogen HZ2 and HZ3 atoms of 2 lysine
> residues (1.39714nm) is 0.00286nm = 0.0286Ang,
> Since this distance is smaller than bond distance between hydrogen and
> nitrogen which is ~1.0Ang, So will this effect the results of the
> simulations?
> Kindly let me know whether I need to redo the simulation again? or is there
> any way to correct this or can it be ignored?
>
> Thanking you
> With regards
> M. Kavyashree
>
>
> On Mon, May 30, 2011 at 10:36 AM, Kavyashree M <hmkvsri at gmail.com> wrote:
>>
>> Hello sir,
>>
>> I had used a dodecahedron cell for simulation. I have run
>> the simulation for 100ns, did you man I have to restart the
>> simulation again?
>>
>> Thanking you
>> Kavya
>>
>> On Sun, May 29, 2011 at 5:40 PM, Tsjerk Wassenaar <tsjerkw at gmail.com>
>> wrote:
>>>
>>> Hi Kavya,
>>>
>>> > "shortest periodic distance is 1.39714 (nm) at time 21824 (ps),
>>> > between atoms 2062 and 3688"
>>> > where 2062 is a protein atom and 21824 is a water molecule.
>>>
>>> 21824 is the time in ps at which the two atoms indicated, 2062 and
>>> 3688, are at the short distance given. You can dump the frame with
>>> trjconv and have a look. Probably your molecule stretched, or you
>>> solvated in a rectangular box and the protein rotated. In the first
>>> case, set a larger distance, in the second, use a rhombic
>>> dodecahedron.
>>>
>>> Cheers,
>>>
>>> Tsjerk
>>>
>>>
>>> --
>>> Tsjerk A. Wassenaar, Ph.D.
>>>
>>> post-doctoral researcher
>>> Molecular Dynamics Group
>>> * Groningen Institute for Biomolecular Research and Biotechnology
>>> * Zernike Institute for Advanced Materials
>>> University of Groningen
>>> The Netherlands
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>
>
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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands