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

zifeng li lizifeng7 at gmail.com
Tue Jul 3 16:47:25 CEST 2012

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,


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