[gmx-users] Max #atoms in a charge group: 68 > 64

[Berk Hess]

Hi,

Charge group neutrality is not an issue when you use PME.

In Gromacs 4.0 grompp would print the following message:
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 artifacts.
For efficiency and accuracy, charge group should consist of a few atoms.
For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc.

Simply follow this rule which groups a few atoms which are close in space.


> Date: Mon, 26 May 2008 23:04:55 +1000
> From: Mark.Abraham at anu.edu.au
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Max #atoms in a charge group: 68 > 64
> 
> Samuel Coulbourn Flores 花山 wrote:
> > So, is it generating the charge groups based on residue numbering?
> 
> I said to look at your .itp/.top file... below you've pasted your .pdb 
> file. I can't tell what your charge groups look like...
> 
> >  Can 
> > I solve the problem by just editing the residue number column such that 
> > the ligand is now composed of two "residues"?  If not, how should I 
> > specify how the molecule is to be broken up into charge groups?  How 
> > strict is the requirement that the charge be an integer?  It seems 
> > unlikely that any subset of the molecule will have net integer charge.
> 
> That all depends how you generated the topology in the first place.
> 
> Non-integral charge-groups with group-based cut-offs will make strict 
> energy conservation difficult/impossible, though whether that has much 
> effect depends on other stuff. I've no idea if this 64-atom limit is 
> just a weird genion thing, or a problem you'll see with mdrun too...

This is an mdrun limitation.
The exclusions for neighbor searching are set with flags in an unsigned long,
which is 64 bits.

In 4.0 grompp will give a warning for charge groups larger than 10 atoms.

Berk.


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