[gmx-users] How to assign charge group for ester?

[Peter C. Lai]

You neglected to mention what Force Field you are using.

See Also: http://lists.gromacs.org/pipermail/gmx-users/2011-April/060752.html

On 2012-07-03 10:47:25AM -0400, zifeng li wrote:
> Dear users,
> 
> I use gromacs version 4.5.4 and is building residues of my own polymer which
> has a ester group (COOR). Should I consider the ester as one neutral
> group or split it into two groups( -COO and -R) ?
> 
> Here's some information I find:
> 
> 1. Should consider them as one group. Based on the fact that Gromacs
> consider a charge group to be a particle so that if I make a
> non-neutral charge group, the total charge within a verlet list might
> not be 0 if
> these two groups are not included in a list at the same time.
> 
> 2. Should split into two groups. First, on Gromacs website, it is said
> the charge group usually includes 4 or less atoms. Second,
> in aminoacids.rtp file, I find some aminoacids, like Asn, which do
> have a non-neutral charge group.
> 
> Would this make a difference?
> 
> Thanks in advance,
> 
> -Zifeng
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Peter C. Lai			| University of Alabama-Birmingham
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