VMD-L Mailing List

From: JC Gumbart (gumbart_at_physics.gatech.edu)
Date: Mon Nov 14 2016 - 23:20:09 CST

Can you first say precisely which version of vmd you are using? We found a
bug for repeated runs of the bond /angle optimization routine last winter.

Also, lower objective values are better.

Best,
JC

On Sun, Nov 13, 2016, 4:34 AM Ern Ong <Ern.Ong_at_student.adfa.edu.au> wrote:

> Hi,
>
>
>
> This is my first time using ffTK plugin to perform bond and angle
> optimization. I have been going through the ffTK tutorial and forums but I
> still can’t grasp the way to determine whether the obtained bond and angle
> parameters are optimized or not. For charge optimization, I adopted the
> SA-DH method with multiple rounds of SA and followed by DH. However in bond
> and angle optimization, I found that the values change a lot with each
> round of either SA or DH. The following is the questions.
>
>
>
> 1. Is it okay for me to run a long SA (probably T=25, Tsteps=100
> and Iter=100 as one did and shared in this vmd forum) and assumed that the
> outcome values are optimized?
>
> 2. Actually how does the final objective value work out? Does it
> mean that the higher final objective value the more optimized it is?
>
>
>
> Thanks for the help.
>
>
>
> Regards,
>
> Ernest
>