[gmx-users] genconf

[Payman Pirzadeh]

Hello,
I minimized the initial output (from another simulation) first; then I
replicated it. This time, the minimization of the bigger box was done more
easily! I ran an MD simulation with the bigger box and after 6 hours, it has
not crashed yet.
But, I have a question. When we replicate a box, and in the primary box one
molecule is dissected into pieces due to pbc, will GROMACS return the
molecules to its original shape during MD run or not?
I believe, without minimization, these dissected pieces will remain in the
middle of the box and interfere with their replicated versions. Maybe,
'genconf' should be modified for such replications to maintain the pbc
between the new molecules at the boundaries and fix the problem with the
particle in the middle of the new bigger box!

Payman 

-----Original Message-----
From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
On Behalf Of Payman Pirzadeh
Sent: July 22, 2009 9:22 AM
To: 'Discussion list for GROMACS users'
Subject: RE: [gmx-users] genconf

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

Payman

-----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
structure
> 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.

Mark
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