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

rama david ramadavidgroup at gmail.com
Sun Nov 11 10:51:00 CET 2012

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 )

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..???

As per your previous reply,

The confusion likely arises from the fact that you're selecting "Protein,"
which actually contains multiple molecules, rather than a single protein
molecule.  Atoms can come pretty close during a simulation, especially if
they are involved in, for instance, hydrogen bonds.

These means whenever I have to check the protein pbc , I have to make the
index file for each chain, and have to select the pbc for that???

Please accept my apology if I repiting  the same  questions. but it is
really confusing to me..

With best Wishes and Regards..
Rama david

On Sun, Nov 11, 2012 at 12:47 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

> On 11/10/12 10:22 AM, rama david wrote:
>> Thank you justin,
>> I actually check these file in vmd by seeing its periodic image , but
>> I not seen any problem in PBC.
>> As per you, If protein contain multiple chain, I have to make the index
>> group for each one.
>> Then I have to check each one by g_mindist -pi   Is these right???
> I suspect that would be more appropriate.
>  But what wiil be the problem if I used the whole group????
>> Still I not get the your explanation..Pardon me, but please explain it
>> again??
> I don't know how to say it differently.  The minimum image convention,
> periodicity, and neighbor searching are all covered in almost every
> simulation textbook, and some elements are described on gromacs.org and
> in the manual.
> -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>

More information about the gromacs.org_gmx-users mailing list