VMD-L Mailing List

From: Amira Yu (amirayuyue_at_gmail.com)
Date: Thu Nov 05 2015 - 07:20:32 CST

Dear Pawel,
  Thank you so much.
Regards,
Yue

2015-11-05 3:04 GMT-05:00 Pawel Kedzierski <pawel.kedzierski_at_pwr.edu.pl>:

> Dear Yue,
> My guess is that this could be simply a sum of rounding errors as the
> charges are saved with 3 decimal places.
> You could manually correct this on one atom or distrubute +0.001 over
> five, the button "Adjust charge" is meant for this.
> Not a big deal how you do it as atomic charges in CHARMM FF usualy have
> the precision to hundreths only.
> Regards,
> Pawel
>
> W dniu 04.11.2015 o 21:05, Amira Yu pisze:
>
> 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.
> Best regards,
> Yue
>
> 2015-11-04 14:51 GMT-05:00 Mayne, Christopher G <cmayne2_at_illinois.edu>:
>
>> Yue,
>>
>> 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.
>>
>> HOWEVER,
>>
>> 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.
>>
>> Regards,
>> Christopher Mayne
>>
>> > On Nov 4, 2015, at 9:09 AM, Amira Yu < <amirayuyue_at_gmail.com>
>> 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
>
>
> 

-- 
Chemical Engineering
YU Yue
859-536-6507