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

[Justin Lemkul]

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

========================================