[gmx-users] large charge group
gmx3 at hotmail.com
Thu Nov 20 08:32:18 CET 2008
No, it does not need to be integer.
With PME it does not matter at all.
With cut-off or reaction-field it is better to have neutral
charge groups when possible, but not at the cost
of making enormous charge groups.
Charge groups should preferable consist of 2, 3 or 4 atoms
which are very close together in space.
Date: Thu, 20 Nov 2008 09:29:46 +0800
From: qiaobf at gmail.com
To: gmx-users at gromacs.org
Subject: Re: RE: [gmx-users] large charge group
Should the total charge for one charge group
be necessarily an integer, such as 0, 1, -1?
If I understand correctly, the answer is yes.
However in this case, the large charge group always happens
except opls-aa force field.
收件人： Discussion list for
主题： RE: [gmx-users] large
The charge groups "only" affect the
which in practice means they affect everything.
Gromacs atoms in two different charge groups will only interactions
center of geometry of the two charge groups is within rlist.
case scenario, which has happend to several people, is:
A molecule with a
radius of about 0.5 nm is one charge group.
If the cut-off is 1 nm, two
molecules will only really start interacting
when they already
In 4.0 I put a check on large charge groups.
If you have
charge groups of more than 10 atoms, grompp will now
warn you with:
largest charge group contains %d atoms.\n"
"Since atoms only see each other
when the centers of geometry of the charge groups they belong to are within the
cut-off distance, too large charge groups can lead to serious cut-off
"For efficiency and accuracy, charge group should consist of a
"For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2,
> Date: Wed, 19 Nov 2008 10:01:01
> From: sunnytov at gmail.com
> To: gmx-users at gromacs.org
Subject: [gmx-users] large charge group
> Hello All
> Recently I have figured out the biggest problem that made my system
> I have parameterized a molecule pretty similar to octane. A
> charge group used to be assigned to this molecule. With 1 nm
> distance for LJ interaction and the direct space for
> interaction, the system underwent severe volume
fluctuation and at the
> end crashed due to enormously large short range
> energy. The problem was temporarily resolved by
using greater cut-off
> distance such as 1.4 nm. But this fixation was not
perfect when I put
> this molecule into more complex system. Regardless of
> distance even to 1.8 nm did not solve the problem. The
> always terminated due to large coulomb energy even though no
> contact or any weird structure was observed at that
> With the help of many experts, I have made a single
charge group into
> three smaller charge group, which magically fixed all
the problem that
> I have had for almost 2 years. I know that charge group
is only used
> for neighbor search. Can anybody tell me how the size of
> can influence the interaction between atoms depending on
> complexity of the system and cut-off distance??
Thank you in advance
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