From: "X.Periole" <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users <gmx-users@gromacs.org>
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Subject: Re: [gmx-users] How do Charge Groups work?
Date: Wed, 28 Jun 2006 20:29:17 +0200
I had a system where I have no charges in it, but I do have Lennard-Jones
non-bonded interactions. I've noticed that I get different values for the
Lennard-jones interaction energy differs depending how I split the system
up into charge groups (as the charge group concept is kinda abitrary in a
system with no charges), this can not be right surely?
As I understood it the charge groups were used to help compile the
neighbour lists, but what I want is all the atoms within my cut-off radius
to be in my pair-list (for that atom). Is there an option to ignore the
charge groups? I find I get bigger Lennard-Jones interactions if I put my
whole system into a charge group that if I split it up, but I need to
split it up for my larger systems. Is there a way to increase the maximum
number of charge groups? And is this a good idea?
You should check the manual for the option allowing a atom
base cutoff, I am not sure it actually exist.
A crude way to fix it would be to define each atom as a
seprate charge group.
This is not a crude way to fix it, this is the only and proper way to fix
it.
But you will still have a cut-off and your simulations will become slower
due to more expensive neighbor searching.
It is usually better to use shifted LJ interactions (see the manual),
than you can also use larger "charge" groups again to speed up the
nieghborsearching, provides that rlist is larger than rvdw to account
for the charge group size and diffusion between neighor list updates.
Berk.
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