[CP2K-user] [CP2K:11251]

[Akshay Malik]

Dear Patrick,
Since I have done AIMD of simple ions in water that is out of 64 water
molecules replaced one water molecule and placed H+ ion in it so i am
expecting to see grotthus mechanism. I am attaching the input files and
trajectory files. Please give it a quick look and reply if I am doing
something wrong.

Yours sincerely
Akshay Malik
 WATER-pos-1.xyz
<https://drive.google.com/file/d/1r2HPG-MvTK6UvZFjgXnM-IkEfZhSIeiy/view?usp=drive_web>
 water.inp
<https://drive.google.com/file/d/1SUH4LUEqy1bAZ0AiOrx0gATttp7K4szy/view?usp=drive_web>
 wateralter.xyz
<https://drive.google.com/file/d/1mKGUwOqDbGH49Un4ciK2Kc1nPTdMRMxe/view?usp=drive_web>

On Mon, Feb 11, 2019 at 6:34 PM Patrick Gono <patric... at gmail.com> wrote:

> Dear Akshay,
>
> A visualization software is just that -- a tool that allows you to
> visually inspect the simulated trajectory. If no proton transfer happened,
> there is nothing to visualize. Assuming that there is some proton transfer
> happening, the CPK representation should be actually the best. Here, the
> bonds are displayed between close-by atoms in the initial configuration,
> and then remain during the simulation. Hence, if a proton did move from one
> water molecule to another, you should see ridiculously stretched O-H bonds
> in your MD. The Dynamic Bonds representation only uses a very simple cutoff
> distance bellow which a bond is displayed. So, naturally, there will be
> some bond breaking and formation of new bonds during the course of the
> simulation, but it may be hard to spot this using this representation.
> Plus, if you use a large cutoff, hydrogen bonds to neighboring water
> molecules might be shown as real bonds occasionally, which is not what you
> probably are looking for.
>
> If you have dozens and dozens of picoseconds worth of trajectory to comb
> through, and you do not trust the CPK representation for some reason, you
> can also write a short script to analyze the trajectory yourself. For
> example, you could calculate the two shortest bonds for each oxygen atom in
> the first snapshot, and then track the length of these bonds over time. At
> some point, if a proton transfer occurs, the length of one of these bonds
> will exceed a given threshold (say, around 1.3 A). You then simply output
> the snapshot index and go look it up in VMD to see what is happening. But
> this is basically what the CPK representation already visualizes.
>
> Are you sure that proton transfer can be observed in your simulation? Are
> you simulating pure water, or do you also include an extra proton (or
> H3O+)? What parameters did you use for the simulation? How long is your
> trajectory in physical terms -- do you expect to observe proton transfer on
> this timescale? Could you share your CP2K input, initial water structure
> file, and possibly (if size allows) the simulated trajectory, please? You
> can upload the trajectory to dropbox or google drive and send me the link
> if it is too large.
>
> Yours sincerely,
> Patrick Gono
>
> On Fri, 8 Feb 2019 at 13:46, Akshay Malik <akshayma... at gmail.com>
> wrote:
>
>> Dear Patrick,
>>
>> I have used VMD to analyze the trajectory file but I am not able to see
>> the quantum effects such as proton transfer in CPK Representation but in
>> DynamicBonds representation there is some sort of bond making and breaking.
>> Can I consider DynamicBonds representation as quantum effects?
>>
>> On Fri, Feb 8, 2019 at 4:37 PM Patrick Gono <patric... at gmail.com>
>> wrote:
>>
>>> Dear Akshay,
>>>
>>> I suggest VMD, which can be found at
>>> https://www.ks.uiuc.edu/Research/vmd/
>>>
>>> Yours sincerely
>>> Patrick Gono
>>>
>>> On Fri, 8 Feb 2019 at 05:35, Akshay Malik <akshayma... at gmail.com>
>>> wrote:
>>>
>>>> I have done AIMD of liquid water by using cp2k. I want to see the bond
>>>> breaking and proton transfer by grotthuss mechanism. Please suggest some
>>>> visualisation softwares.
>>>>
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