VMD-L Mailing List

From: JC Gumbart (gumbart_at_physics.gatech.edu)
Date: Thu Nov 17 2016 - 11:56:18 CST

Sorry for not replying sooner. Yes, it should be fixed in that version.
Please give it a try!

Best,
JC

On Thu, Nov 17, 2016, 4:39 AM Ern.Ong_at_student.adfa.edu.au <
Ern.Ong_at_student.adfa.edu.au> wrote:

> Hi JC,
>
>
>
> Is the bug being fixed in VMD for WIN32, version 1.9.3 beta 4 (2016-10-28)
> platform? Could you please help to elaborate more details about the bug?
>
>
>
> Thank you.
>
>
>
> Regards,
>
> Ernest
>
>
>
> *From:* Ern Ong
> *Sent:* Tuesday, 15 November 2016 4:33 PM
> *To:* 'JC Gumbart'; vmd-l_at_ks.uiuc.edu
> *Subject:* RE: vmd-l: ffTK: How to determine the optimized bond and angle
> parameters
>
>
>
> I am using the VMD for WIN32, version 1.9.2 (December 29, 2014).
>
>
>
> Regards,
>
> Ernest
>
>
>
> *From:* JC Gumbart [mailto:gumbart_at_physics.gatech.edu
> <gumbart_at_physics.gatech.edu>]
> *Sent:* Tuesday, 15 November 2016 4:20 PM
> *To:* Ern Ong; vmd-l_at_ks.uiuc.edu
> *Subject:* Re: vmd-l: ffTK: How to determine the optimized bond and angle
> parameters
>
>
>
> 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
>
>