[gmx-users] periodic boundary conditions

[David]

On Thu, 2003-12-04 at 17:55, Ilya Chorny wrote:
> I think the current version of gromacs has a bug in it. Download the CVS
> beta version
> I believe it has been fixed.

the mdrun program is OK and energies are too.
May this analysis program has a problem with PBC, but that can probably
by resolved by using trjconv -pbc whole

> 
> Ilya
> 
> 
> -----Original Message-----
> From: gmx-users-admin at gromacs.org [mailto:gmx-users-admin at gromacs.org]On
> Behalf Of xiaoyi li
> Sent: Thursday, December 04, 2003 6:46 AM
> To: gmx-users at gromacs.org
> Subject: [gmx-users] periodic boundary conditions
> 
> 
> 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?
> 
> Thanks in advance!
> 
> Xiaoyi
> Uppsala University
> Sweden
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
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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