[gmx-users] About periodic image of system.......

[rama david]

Thank you for your reply.


On Sun, Nov 11, 2012 at 8:30 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 11/11/12 4:51 AM, rama david wrote:
>
>> Hi justin ,
>>
>> Thank you a lot for your explaination.
>>
>> My opinion  on the working of g_mindist -pi is that when it shows the
>> distance between two atom
>> of the protein is less than vdw cut off ( 1.4 nm ) , then protein see it
>> periodic image, and it is the violation of pbc.
>> Is these is right??? ( That is the shortest Periodic distance should be
>> larger than vdw cut off 1.4 )
>>
>>
> This is correct, when considering a single molecule, i.e. it can't see
> itself. If you have two proteins, and you choose the blanket "Protein"
> group, you haven't determined anything, because now the calculation
> involves multiple molecules.
>
>
>  If it is right, g_mindist say that  The shortest periodic distance is
>> 0.154938 (nm) at time 16162 (ps),
>> between atoms 223 and 3270
>> This is less than 1.4 then Why it is not problem..???
>>
>>
> Because they're in separate molecules.  Did you ever do as I suggested and
> visualize this frame?  It will be immediately apparent that there is no
> problem.  Please refer to textbooks or even simple Google searching for
> explanations of the minimum image convention.  As I said, it is described
> in almost every reference text.
>
>
> -Justin
>
> --
> ==============================**==========
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==============================**==========
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>
> * Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before posting!
> * Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>
>