From: Gianluca Interlandi (
Date: Thu Aug 28 2014 - 00:16:37 CDT

This is normal. There is no problem with it. You have periodic boundary
conditions (implemented like crystal), when the protein leaves the box
from one side, it re-enters from the other.


On Thu, 28 Aug 2014, BIPLAB NANDI wrote:

> Hi All,
> I am running one MD simulation for my system a** a solvated monomeric
> protein. But, some part of the protein is going out of the solvation
> box after 15ns. I am not able to find out the problem in my MD run. I
> am restarting the simulation after every 5 ns run.Is there any problem
> in restart file? If yes, then how to detect? So please help me to
> solve this problem.
> With regards,
> Biplab Nandi

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