[CP2K-user] [CP2K:15744] Re: ab initio BO-MD: hydrated complex

[Victor Volkov]

 Good afternoon, Marcella:

>Your time-step is too large.

Thank you, dear Marcelle
I will test a shorter step.
I think you might got it right,
because,
the instabilities always concern the dynamics of Hydrogen stretchings only,
but they are at the higher frequency range.

> Is there a reason why you use Langevin dynamics rather than a more
standard thermostat?

In the input
for all the atoms
I instruct
DO_LANGEVIN F

Therefore,
I thought the simulation should be B-O
not Langevin.
I suspect that
still
the thermostat to accomodate the dynamiocs is
not well defined.
*Would you give me a hint?  *

"My" current configuration in the input
is according to several examples I found on-line
and some intuitive guess-trials.

The idea is
with least possible compromise
to try to simulate delocalised water dynamics
to interact with the copper ion which is doublet while it is complexed by
aminoacids
This would be the simplest but yet the most comprehencive
simulation to approach a vision of what is going on in comparable complexes
in vivo.

>Are you sure that diagonalization+smearing
>is the most efficient optimisation scheme for your system?

I studied the examples and various inputs on-line.
Indeed, my setting may not be adequate.
Would you recommend to set it different?

During the past 4 days I tuned the ambition a bit down
and started testing a dry complex in vacuum.
It runs well without any issues: please see T0.xyz

Today, I moved one step ahead adding one water
but
this time I do instruct
the three atoms of the water
by Langevin,
while the rest is by BO.

However, I am not sure that in such case as much quantum dynamics
of interaction of water with the copper would be respected:
please see the attached T1a files

Carole and me will acknowledge you advise in the manuscript we are working
on.

Thank you.
Wish you a nice day,
Victor





On Thu, Jul 15, 2021 at 11:29 AM Marcella Iannuzzi <marci... at gmail.com>
wrote:

> Hi Victor,
>
> Your time-step is  too large.
> Is there a reason why you use Langevin dynamics rather than a more
> standard thermostat?
> Are you sure that diagonalization+smearing is the most efficient
> optimisation scheme for your system?
>
> Kind regards
> Marcella
>
> On Monday, July 12, 2021 at 3:08:36 PM UTC+2 vo... at gmail.com wrote:
>
>>
>> good day
>> I wish to ask about the observed structural instability upon BO-MD
>> of a hydrated copper-proline complex.
>> It starts ok, but later hydrogens start to fly away.
>> Thank you.
>> Victor
>>
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