Previous Thread
Next Thread
Print Thread
Page 4 of 6 1 2 3 4 5 6
Re: generating parameters for pyruvate
RD2015 #24363 05/21/10 01:50 AM
Joined: Dec 2005
Posts: 1,535
Forum Member
Offline
Forum Member
Joined: Dec 2005
Posts: 1,535
OK, we're getting somewhere. Here are a few tips:
  • For the OCCC, the shape could be better. I would try adding a 4-fold contribution to improve it. However, be careful not to add contributions with an odd phase. For background information, see the CGenFF FAQ and the private discussion thread I refered to earlier.
  • For the CCCH:
    • You see that the left part of your graph has a constant offset, which makes it more difficult to fit. One way to solve this is to split it in two: one scan for the CCCH (in which only CCCH is constrained) and another one for the OCCC, both of them aligned to their own minimum. The other (more challenging) solution is to first get the shape of the OCCC right (if you take your QM minimum in the OCCC scan and look at the MM energy at that same dihedral angle, there you have your offset...)
    • You currently only have a 3-fold contribution for the CCCH. Keep it that way.

Re: generating parameters for pyruvate
Kenno #24364 05/21/10 03:21 AM
Joined: Jan 2010
Posts: 85
R
RD2015 Offline OP
Forum Member
OP Offline
Forum Member
R
Joined: Jan 2010
Posts: 85
I removed the constraint for the c-c-c-h like you said. Fit looks a little better?

Changing multiplicity for the other dihedral produced strange results. I started getting peaks inside of the wells.

***
By the way, I need to set up explicit solvation and periodic boundary conditions. Offhand can you recommend any good resources?

Thanks again.

Attached Files
scan.tar.gz (634.26 KB, 528 downloads)
scan.jpg (27.38 KB, 695 downloads)
Last edited by RD2015; 05/21/10 04:22 PM.
Re: generating parameters for pyruvate
RD2015 #24366 05/21/10 05:17 PM
Joined: Dec 2005
Posts: 1,535
Forum Member
Offline
Forum Member
Joined: Dec 2005
Posts: 1,535
Originally Posted By: RD2015
Changing multiplicity for the other dihedral produced strange results. I started getting peaks inside of the wells.
Yes. We're trying to reproduce the QM. The QM has peaks inside the wells. One thing you could do is visualize the QM scan and see whether any of the C(sp²) centers became slightly nonplanar around the energy minimum. That is a possible source of the peaks, and in that case, we don't necessarily want to reproduce them.

At any rate, I didn't say changing multiplicity - I said adding a multiplicity, so that you have a 2-fold and a 4-fold term for the same dihedral. There are tons of resources (most importantly, the tutorial) that show how this works. But check the planarity first.

Yesterday, I forgot to look at the scale of the graph. I now discovered it's from 0 to 1 kcal/mol; in other words, the discrepancies around the minimum are are small in terms of energy. As far as I am concerned, the fit is acceptable. But I still think you can get the OCCC even better by adding a 4-fold (and/or possibly a 6-fold, but let's not go there for now).

Originally Posted By: RD2015
By the way, I need to set up explicit solvation and periodic boundary conditions. Offhand can you recommend any good resources?
The script archive comes to mind...

Re: generating parameters for pyruvate
Kenno #24372 05/21/10 10:50 PM
Joined: Jan 2010
Posts: 85
R
RD2015 Offline OP
Forum Member
OP Offline
Forum Member
R
Joined: Jan 2010
Posts: 85
I visualized the qm pdb files. You were right there is a loss of sp2 planarity of about 3 degrees.

Are these parameters good to use now?

***

I have been looking at the scripts from the archive as well as schlick's book. I was just wondering if there is anything else to read for background.

Re: generating parameters for pyruvate
RD2015 #24378 05/24/10 05:17 PM
Joined: Dec 2005
Posts: 1,535
Forum Member
Offline
Forum Member
Joined: Dec 2005
Posts: 1,535
Can you gzip the gaussian output file of the OCCC scan and post it?

Re: generating parameters for pyruvate
Kenno #24380 05/24/10 05:22 PM
Joined: Jan 2010
Posts: 85
R
RD2015 Offline OP
Forum Member
OP Offline
Forum Member
R
Joined: Jan 2010
Posts: 85
It's just over the limit for the forum. So i posted on an external site.

http://ifile.it/nsk86br

Re: generating parameters for pyruvate
RD2015 #24382 05/24/10 05:59 PM
Joined: Dec 2005
Posts: 1,535
Forum Member
Offline
Forum Member
Joined: Dec 2005
Posts: 1,535
While the tiny deviation from planarity might be part of the cause of the "peak inside the well", we don't want to try to reproduce this deviation, because doing so would likely compromise the vibrational spectrum and the transferability. Nevertheless, I'd prefer the shape of the well to be reproduced a bit better. You can use the parameters as they are if you think they're good enough for your purpose, but I'd recommend trying with the additional term(s). It's not a lot of work.

Re: generating parameters for pyruvate
Kenno #24389 05/24/10 07:55 PM
Joined: Jan 2010
Posts: 85
R
RD2015 Offline OP
Forum Member
OP Offline
Forum Member
R
Joined: Jan 2010
Posts: 85
Thanks.

Are you saying I should add in an additional term like:
OG2D2 CG2O3 CG2O5 CG331 (?) 4 0.00

And see if it helps the fit?

***
I added the additional term. Picture is attached.

Attached Files
newscan.jpg (25.59 KB, 691 downloads)
Last edited by RD2015; 05/24/10 08:06 PM. Reason: added the term
Re: generating parameters for pyruvate
RD2015 #24401 05/25/10 04:59 AM
Joined: Dec 2005
Posts: 1,535
Forum Member
Offline
Forum Member
Joined: Dec 2005
Posts: 1,535
Looks like a dramatic improvement, doesn't it? smile

However, something else is bothering me now. Although the picture is very small, it looks to me like the symmetry is broken. What are the final parameters for that dihedral?

Re: generating parameters for pyruvate
Kenno #24406 05/25/10 03:16 PM
Joined: Jan 2010
Posts: 85
R
RD2015 Offline OP
Forum Member
OP Offline
Forum Member
R
Joined: Jan 2010
Posts: 85
CG2O3 CG2O5 CG331 HGA3 0.1200 3 0.00
OG2D2 CG2O3 CG2O5 CG331 0.6450 2 180.00
OG2D2 CG2O3 CG2O5 CG331 0.0800 4 0.00

Page 4 of 6 1 2 3 4 5 6

Moderated by  alex, chmgr, John Legato 

Link Copied to Clipboard
Powered by UBB.threads™ PHP Forum Software 7.7.4
(Release build 20200307)
Responsive Width:

PHP: 5.6.33-0+deb8u1 Page Time: 0.013s Queries: 36 (0.005s) Memory: 0.9944 MB (Peak: 1.1314 MB) Data Comp: Off Server Time: 2020-05-25 17:46:25 UTC
Valid HTML 5 and Valid CSS