[CP2K-user] [CP2K:19305] Re: Ehrenfest dynamics: Glycine

[Natalia K]

Dear Victor,

I am curious, in these calculations, is the total energy ("Cons Qty" in the 
systemlabel.ener file) conserved? What about the case when the temperature 
grows high? What version of CP2K did you use to get the results attached to 
your last email?

Thank you and best regards,

Natalia

On Wednesday, May 31, 2023 at 4:43:57 PM UTC+2 Victor Volkov wrote:

Dear Matthew:
good afternoon.
Sorry to bother once more.
I took Gly and Ala oriented the way that their COO-Ca-N plane is parallel 
to XZ plane
and modeled charge dynamics propagating under such 5 field settings 
{Ex = 0, Ey = 0} no field
{Ex=0, Ey} polarized along Y
{Ex, Ey = 0} polarized along X
{Ex, Ey + P/2 shifted} left circular polarized
{Ex, Ey - P/2 shifted} right circular polarized.

The initial geometries are proximal to the global minimum optimized under 
DFT.

I attach an image where I sum-up the results.
When there are no fields, apparently, there is just the equillibration: 
energy flows into kinetic populating vibrations,
and there is the intra-molecular H dynamics between the terminals.

Field polarized along X (parallel to the COO-Ca-N plane ) makes 
thermalization slowe.

Field polarized along Y (perpendicular to the COO-Ca-N plane) introduce 
strong anticorrelation of side groups charges for Gly,
but it does not slow down the thermalization for Gly.
Instead, in the case of Ala, the temperature and the kinetic energy explode 
at a certain point - the shake up start to break the molecule.
At the same time, the shake up for the potential energy is about the same 
as when field is parallel to X.
This is peculiar since one could think that shaking between the terminals 
should have larger effect.  

Using CD polarized light, phase of charge modulations of the side groups, 
only, reflect "chirality" of the drive.
In the case of Ala, cp2k simulates both, the temperature and the kinetic 
energy explode at a certain point.

I simulate using energy constraining NVE and instructing T=300K.
Potential energy does change smooth, always.

I wish to ask your opinion: the increase of temperature as cp2k simulate is 
it a signature
of investing energy into molecule that it start to break it apart 
"properly",
or it is a "proper" mis-performance of the NVE part of the equations,
or it is a signature of the equations collapse?

I doubt about the third because I tested increasing the amplitude of the 
drive: at certain point
the potential energy start to show a ripple.
The data I attach here does show potential energy to vary smoothly.

Therefore, I think it is likely that the molecule is getting very hot.

Thank you.

With best,
Victor  
   


 

On Mon, May 22, 2023 at 4:56 PM Matt Watkins <mattwa... at gmail.com> wrote:

Hi Victor,
from your setup the main things are:

   - the cutoff is too small - should be set like a standard DFT 
   calculation - something around 400 Ry and the REL_CUTOFF to 60 Ry or 
   similar.
   - the timestep is very aggressive. If you plot your energy as function 
   of time I think you will see the conserved quantity drift badly at some 
   point in your simulation and then it explodes. Try something like 
   - stepsize [au_t] 0.1
   
Matt

On Friday, 19 May 2023 at 07:48:32 UTC+1 Victor Volkov wrote:

Good day.
I am exploring molecular dynamics under field.
I set glycine at the center of a box,
and suggested Ehrenfest dynamics with a time step of about 0.04 fs,
while the custom field file sets the external field to ZERO. 
The simulation proceeds alright, till the time-frame 500, after which
there is a peculiar structural "expansion".
*Q1: Would you comment this?*
Also, I attach a fragment of the momentum file:
CP2K prints reference point position to be "chaotic",
while I select REFERENCE COAC: since the atomic charges of the glycine, 
the reference point should be next to the C-alpha atom. 
*Q2:  would you comment on the usage of the setting I selected?  *
Thank you.
Victor

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