[gmx-users] periodic boundary condition

[David van der Spoel]

On Wed, 2003-04-30 at 11:18, Itamar Kass wrote:
> 
>    Dear all, I know I will sound like I am a stupid (and maybe I am), but I did
> not sure regarding the periodic boundary condition setting.  As I see it, if I
> do not write something spacial in the mdp file, the system is automatically set
> the boundary.  But when I run gromacs on my system, some atoms are out of the
> simulation box.
>    I wanted to now, first theoretically, if the boundary are properly set how
> can it be?  As I understand it, if an atom x moves through a wall into box y
> (from the simulation box), the same x atom, from the opposite box (to the y box)
> should enter the simulation box.  Hence the amount and composition of atoms in
> the simulation box should remain the same.
>    Second, if I should set the periodic boundary condition how this is handle in
> the mdp file?  Is there any tutorial regarding it?
> 
pbc = xyz

check your md.log file to see what you have used.
you can have half a protein sticking out of the box because gromacs
always writes complete molecules, not broken ones.

>          Thank in advance, Kass.
> 
> 
> ********************************************
> Computers are like airconditioners... They don't work well with Windows
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> 
> ===========================================
> | Itamar Kass
> | The Alexander Silberman
> | Institute of Life Sciences
> | Department of Biological Chemistry
> | The Hebrew University, Givat-Ram
> | Jerusalem, 91904, Israel
> | Tel: +972-(0)2-6585146
> | Fax: +972-(0)2-6584329
> | Email: ikass at cc.huji.ac.il
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-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell & Mol. Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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