[gmx-users] What's the effect of non-neotron charge group?

zifeng li lizifeng7 at gmail.com
Tue Jun 26 21:37:07 CEST 2012

Dear Gromacs users,

I use gromacs version 4.5.4 and build residue of my own polymers which
has a ester group (COOR). From aminoacids.atp database, I found the
partial charge of each atom, where the carbolic group COO- is not
neutron and has to be neutralized by a methyl group. Should I consider
the ester as one neutral group or split it into two groups?

Here's some exploration I have done:

1. Should consider them as one group. Based on the fact that Gromacs
consider a charge group to be a moving particle so that if I make a
non-neutral charge group ( i.e., COO- , methyl connected to it as two
charge groups), the total charge of 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. Considering this,
it seems that I have to split the ester group into two groups. Second,
in aminoacids.rtp file, I find some aminoacids, like Asn, which do
have a non-neutral charge group.

Would this really make a difference?

Thanks in advance,


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