When I am giving rotational move or translational move to the C02 molecule. During this move one of the atom of CO2 goes out of the simulation box. How should I take care of these types of problems.
Simulation box is not a box but it's the periodic conditions. There are no boundaries, respectively, nothing can come out of them. No problem.
Simulation box is not a box but it's the periodic conditions. There are no boundaries, respectively, nothing can come out of them. No problem.
How you deal with this depends a lot of the details of your algorthm and how you store the molecular/atomic positions. There should be no problem with one part of the molecule being on the other side of the box as long as you take the PBC into account when calculating interatomic distances by using the minimum image convention http://en.wikipedia.org/wiki/Periodic_boundary_conditions#Practical_implementation:_continuity_and_the_minimum_image_convention
You might be interested in this algorithm for the center of mass http://en.wikipedia.org/wiki/Center_of_mass#Systems_with_periodic_boundary_conditions Although if your CO2 molecules are rigid then the center of mass is obviously always on the carbon.
There are a boundary condition applied to keep the molecules or atoms on the box, it seems there is a mistake in your applied program is it a Monte carlo Simulartion, I advic you to ckeck the coding of the program and see the functions used , there is a nice book for these things, see the referrences in my paper , Applied Surface Science, 256, 1443 (2009)
(PBC) are a set of boundary conditions which are often chosen for approximating a large (infinite) system by using a small part called a unit cell.
In simulations of solid systems, the strain field arising from any inhomogenuity in the system will be artificially truncated and modified by the periodic boundary.
Hey,
In simple words - the first thing you need to consider is the ensemble type that you are using to investigate your system. Past this point - you need to ensure that the Number of particles in your system remain more or less the same - as the most popular ensembles used are NVT/NPT/NVE - N being the number of particles. Are you working within an established program - if you are e.g. charmm has images - so if the boundary conditions have been properly implemented within your code - the number of particles in your principle box will remain more or less the same. How this will happen is as a complete molecule moves out of the system - another one will move in (This doesn't happen on a 1 to 1 basis but an average is usually constant).
This PBC is different from co-ordinate wrapping which basically just translates a point by a certain amount when it attempts to cross a boundary - which I am guessing is not what you are doing. If you want your molecule to not disappear you can use Spherical boundary conditions which have a force potential associated with them. In that case if a molecule tries to pass through it - it will experience a potential pushing it back keeping it within the system.
So - to sum it up - if you define your PBC - the program (like CHARMM, NAMD) will automatically fix everything - even though you see something disappearing, the total number of particles in the system will more or less remain the same.
Hope this clarifies things.
Good luck.
Best,
/A
OK ...THANKS EVERY1 FOR YOUR VALUABLE SUGGESTIONS.
I GOT MY ANSWER .....
IF I AM APPLYING PERIODIC BOUNDARY CONDITION WITH MINIMUM IMAGE CONVENTION. THEN THERE IS NO PROBLEM.
Yes if you are applying them correctly - which basically just means that in case of your minimum image convention your cut off should take into account the total size of the principle cell. If you have that in order - disappearing Molecules are ok.
Good Luck.
Best,
/A
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