[gmx-users] periodic boundary conditions

[Anton Feenstra]

xiaoyi li wrote:

> Hi all,
> 
> I use periodic boundary conditions in my simulations by Gromacs. It said
> in the manual that only one - the nearest image of each particle is
> considered for short-range non-bonded interaction terms during the
> simulations (called minimum image convention).
> 
> However, when i try to analysize the trajectory and calculate the
> distance between two planes by g_sgangle, I found that the results
> aren't got from the nearest image but the images in one cell. So the
> results cannot be used directly whenever particles are near the
> boundary. 
> 
> My question is: When we calculate the total energy by g_energy, is the
> result got from images in one cell? If so, are there any method to get
> the total energy and the distance from the nearest images? 

g_energy doesn't calculate energies, it only retrieves them from the
energy file where they have been put by mdrun. So these are the 'real'
energies, taking any general and special conditions in the simulation
into full account, obviously.


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
|             | "If You See Me Getting High, Knock Me Down"           |
|             | (Red Hot Chili Peppers)                               |
|_____________|_______________________________________________________|