[gmx-users] About charge group(Mark)

wuxiao xiaowu759 at hotmail.com
Thu Jun 25 04:13:34 CEST 2009

Dear Mark and other gmx users,

  Thank you for the reply. In practice, I have a dendrimer in hand and find the two parts on two different neighbour residues have total charge 0. I think the two parts can be set as a charge group. My questions (1) and (2) become: is it reasonable to do so? Also to set all of them manually is not a trivial thing. My question (3) becomes: How to do so?



Chaofu Wu


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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