[gmx-users] wrong charge assignment(?) on ATP in rtp file

chris.neale at utoronto.ca chris.neale at utoronto.ca
Wed Jul 7 20:35:34 CEST 2010


"It seems that I do not need to care about decimal total group charges  
as I am planning to use PME."

-- well, find it in the literature first!

-- original message --

Dear Chris,

I really appreciate your comment.
Can you provide a reference for the idea that the charge groups must  
have integer charge?
I actually do not have any critical literature for the idea of  
“whole number rule”;
1) In the item of “Charge group” of the “GROMACS  
USER MANUAL, ver.4” in chapter 3, a charge group is described  
as follow “A charge group is a small set of nearby atoms with  
an integer net charge.”
2) So far, I have not seen decimal total group charges.

Hence I had thought that the rule is an algorithm requirement or an  
empirically obtained criterion or something.  It seems that I do not  
need to care about decimal total group charges as I am planning to use  
PME.
Can you find the original reference for the G53a6 ATP parameters?
Unfortunately I could not find the original paper.  It is also  
unavailable who made the parameter when and how.  If you have  
information about the parameters, could you please let me know?

Best regards,
Shuntaro.




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