VMD-L Mailing List
From: Amira Yu (amirayuyue_at_gmail.com)
Date: Wed Nov 04 2015 - 14:05:26 CST
Dear Dr. Mayne,
Thank you so much for you replying, I think I clicked “Calculate from PSF”
button, otherwise the optimization process would give me error message.
And I think biphenyl is well established in CGenFF but not with the
hydorxyl subs. Even from the ParamChem, the charges and parameters are
still having relative big penalties for hydroxylbiphenyl, that is why I am
going througth the parameterization process. In terms of assigned
constraints, I did use the default value (-1, 1) which is a fairly large
range, but I am not sure whether this constraints will lead to a non-zero
sum of charges.
Thank you again.
2015-11-04 14:51 GMT-05:00 Mayne, Christopher G <cmayne2_at_illinois.edu>:
> I don’t know for sure what the problem is; however, my best guess is that
> there is a problem how you assigned the charge groups (Charge Constraints
> box) and/or didn’t click the “Calculate from PSF” button. I have seen in
> very rare cases an optimized charge total that doesn’t exactly match
> computed the “optimized sim” from the Charge Constraints section, which is
> the purpose of the “Adjust Charge” box in the Results section.
> I’m not really sure that you need to be doing parameterization at all, as
> hydroxybiphenyl is a very simple organic molecule that is well represented
> in the CGenFF.
> Christopher Mayne
> > On Nov 4, 2015, at 9:09 AM, Amira Yu <amirayuyue_at_gmail.com> wrote:
> > 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
-- Chemical Engineering YU Yue 859-536-6507