VMD-L Mailing List

From: Smith, Harper E. (smith.12510_at_buckeyemail.osu.edu)
Date: Fri Mar 26 2021 - 13:55:44 CDT

Hi Brian and Jason,

To be more specific about my problem, MP2 gives me a nonplanar guanidinium group, yet with HF it is planar (especially planar with implicit water). I am not a chemistry person, but my labmates have advised me that a bent guanidinium would not be the optimal structure (maybe things are different in vacuum?). On this same topic, could someone help me understand why the FFTK/CHARMM calculations are in vacuum instead of water?

I did try a frequency analysis, which confirms that the structure has converged (based on the final "Converged? YES/NO" table in the Gaussian output).

Looking at some old simulations I have done with CHARMM36m, the arginine guanidinium groups do deviate from planar. Frankly, I doubt that the bending is more extreme in my MP2-optimized structure. But even if the structure is possible, isn't it important to start with something ideal for parameter generation?

Best,
Harper Smith
________________________________
From: Jason Smith <jason_smith_18_at_sfu.ca>
Sent: Friday, March 26, 2021 2:25 PM
To: Smith, Harper E. <smith.12510_at_buckeyemail.osu.edu>; vmd-l_at_ks.uiuc.edu <vmd-l_at_ks.uiuc.edu>
Subject: Re: Switching from MP2 in FFTK?

Hey Harper,

I'd recommend against deviating from the HF, MP2 requirements - You need the obtained parameters to be compatible with the rest of the forcefield after all. I'm not certain what you mean by 'wrong' geometry in MP2. If you got convergence, then you have a local minima in MP2 (most likely, although you need to run a frequency analysis to find out...). Perhaps there is another way to segment the molecule to have less contaminating issues from the 'bad' dihedrals?

Either way, it sounds at first glance like you will need to run some more MP2 calcs.

Cheers,

-
Jason Smith
Post-Doctoral Fellow
Robert N. Young Lab, Simon Fraser University
8888 University Drive, Burnaby, BC, V5A-1S6
Canada

________________________________
From: owner-vmd-l_at_ks.uiuc.edu <owner-vmd-l_at_ks.uiuc.edu> on behalf of Smith, Harper E. <smith.12510_at_buckeyemail.osu.edu>
Sent: Friday, 26 March 2021 9:15:10 AM
To: vmd-l_at_ks.uiuc.edu
Subject: vmd-l: Switching from MP2 in FFTK?

Hi mailing list,

It seems like FFTK is designed specifically for use at the MP2 level of theory. Unfortunately, my small molecule is optimized to the wrong geometry at MP2, but something much closer at HF (especially if I add implicit water).

It seems like my options are:

  * Stick to the protocol by proceeding with the flawed geometry that comes from an MP2 optimization
  * Deviate from the protocol by switching to HF/SMD, but use a clearly better geometry

Does anyone have any experience with this? Which of these options should I prefer? It seems like either option will give non-ideal results, but I lack the experience to judge which is better.

Best,
Harper Smith