[gmx-users] Minimum periodic distance

[Kavyashree M]

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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