[CP2K-user] [CP2K:11244]

[Patrick Gono]

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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