[gmx-users] About charge group

Mark Abraham Mark.Abraham at anu.edu.au
Thu Jun 25 03:40:09 CEST 2009

wuxiao wrote:
> Dear gmx users,
>    Recently, some questions puzzle me too much. While reading many 
> resources, I can not think out. Therefore, I would like to turn for this 
> mail-list. These questions are as follows:
>    (1) The total number of partial atom charge by summing the residue 
> must be zero? 

No, but it would usually be a good idea, lest some polymer end up with a
non-zero charge.

>    (2) It can set several atoms into a charge group, which is neighbour 
> covalent but on different residues?

It could, but in general this would prohibit use of pdb2gmx.

>    (3) There are some tools, which can help set the number of charge 
> group (cgnr)?

No. For example, they are coded in the .rtp file and pdb2gmx slavishly
copies them.


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