VMD-L Mailing List

From: Amira Yu (amirayuyue_at_gmail.com)
Date: Wed Nov 04 2015 - 09:09:39 CST

Hi All,
  I am doing a charge optimization in ffTK for a neutral charged aromatic
molecule (hydroxylbiphenyl). I assigned the initial charges according to
the CGenFF parameters. Deleted the aromatic H atoms (0.115 according to
CGenFF). However, after running the charge optimization several times
(first run with Stimulated annealing and followed with downhill), the
charges seemed converged. When I checked the total sum of the charges, the
total sum was not zero, it was -0.005 (I set the tolerence in the "advanced
settings" to be 0.001). I used the similar method for 2-2 biphenol which is
a highly symmetric molecule, the sum of the charges are very close to zero
(3E-16). I am not sure whether the non-zero sum of charges represents the
charge optimization is still not good or it was okay for some kind of
tolerence. The other reason why I am concerned the sum of charges is that,
I have to use CHARMM later on to build a solvate system, and this non-zero
charge will let CHARMM show some level-zero warnings (the sum of charges is
not an integer).
  Thank you in advance.
Best regards,
Yue 

-- 
Chemical Engineering
YU Yue