[gmx-users] genconf

Payman Pirzadeh ppirzade at ucalgary.ca
Wed Jul 22 17:22:16 CEST 2009

Thanks a lot Mark! I will run the system for equilibration and then try to
replicate it. I will keep you guys posted.


-----Original Message-----
From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
On Behalf Of Mark Abraham
Sent: July 21, 2009 11:01 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] genconf

Payman Pirzadeh wrote:
> Yes and no!
> Sometimes there is an overlap, but sometimes I could find nothing! In the
> simplest case, how can we avoid overlaps in a way that the crystal
> is maintained under pbc?
> Can the option "-dist" help here?

Replicating a box that was not designed for periodicity will always have 
this problem. Whether the box is too small or two large, there will 
either be steric clashes, or vacuums that will need filling. The general 
solution is to equilibrate your box under PBC prior to replication. Now 
the box size and the atomic spacings will be plausible, and the 
replication will not of necessity introduce artifacts.

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