[CP2K-user] [CP2K:14078] How to make coordinate file

[sumit agrawal]

Dear Lucas Loderio and Travis

Thanks for the suggestions. I have tried packmol today. In packmol I
can easily make my input geometry and it is very easy to use. I have given
a tolerance value equal to 2 for my above system. Now I can use this input
file for cp2k calculation.

I have one more question: Should I need to perform geo-opt before computing
the vibrational spectra?

Thanks a lot !!!


On Fri, Oct 16, 2020 at 6:54 PM Travis <polla... at gmail.com> wrote:

> Hi,
>
> To add, as a general practice for condensed phase simulations: build a box
> with Packmol and equilibrate it with a classical force field that does
> reasonably well. Use several well-separated snapshots as initial
> configurations for CP2K. For a simulation with a simple solute in it,
> well-separated might mean configurations taken every 2*tau or 3*tau where
> tau is the solvent-solute residence time. This can be short for weakly
> interacting species but many nanoseconds for very strongly interacting
> species or viscous solutions. You may even need to simulate at elevated
> temperatures to reduce the residence time. If you don't know how to compute
> that from the output of your preferred molecular dynamics code, I would
> recommend LAMMPS for which there are many community-developed analysis
> tools. Ed Maginn's group at Notre Dame has a well-rounded analysis suite
> hosted on Github... PyLat or something like that. There's no unique answer
> for what 'well-separated' means, this is just the criteria we use.
>
> For this particular system, since it sounds like this might still be an
> exercise, you can take one of the CP2K example files for (H2O)128, convert
> one of the H2O to methanol using Avogadro or GaussView, and run from there.
> If the concentration really matters for your case, then go the Packmol and
> classical force field route.
>
> -T
>
> On Friday, October 16, 2020 at 1:59:54 PM UTC-4 Lucas Lodeiro wrote:
>
>> Dear Sumit Agrawal,
>>
>> I suggest the Packmol software to construct initial configurations, It is
>> a simple and tractable, where you can decide where put some particular
>> molecules, the siz of the box, the number of different molecules, and there
>> is a criteria to ensure your molecules are not so near between them. For
>> little boxes is useful, but for big systems is mandatory to use a program
>> like Packmol.
>> http://m3g.iqm.unicamp.br/packmol/home.shtml
>>
>>
>> Regards
>>
>>
>> El vie., 16 oct. 2020 a las 14:20, Vasyl Stotskyi (<vas... at gmail.com>)
>> escribió:
>>
>>> Dear Sumit Agrawal,
>>> Sure, if you can save it in one of avogadro readable formats (.xyz,
>>> .cif, ....).
>>> If initial geometries of molecules in gaus view will be fine, then you
>>> don't have to optimize it in Avogadro, i.e. if you will not have O-H bonds
>>> with more than 1.5 angstrom  length or overlap of molecules, or huge vacuum
>>> between molecules. Avogadro optimization is the most useful only for such
>>> bad cases.
>>> Best regards,
>>> Vasyl
>>>
>>> On Oct 17 2020, at 12:40 am, sumit agrawal <sum... at gmail.com> wrote:
>>>
>>> Dear Vasyl,
>>>
>>> Thanks for the answer. So I have to manually draw 100 molecules of water
>>> and methanol in Avogadro? Actually,  I am more comfortable with gauss
>>> views. So can i make a coordinate file in gusse view then pre optimize in
>>> the avogadro ?
>>>
>>>
>>> [image: Sent from Mailspring]
>>> On Fri, Oct 16, 2020 at 9:04 AM Vasyl Stotskyi <vas... at gmail.com>
>>> wrote:
>>>
>>> Dear Sumit Agrawal,
>>> You can create some model in Avogadro. There you can pre-optimize it
>>> with force fields, and save as .xyz file. In CP2K, then you can read
>>> coordinates from .xyz file. Please, read manual for this (
>>> https://manual.cp2k.org/cp2k-7_1-branch/CP2K_INPUT/FORCE_EVAL/SUBSYS/TOPOLOGY.html
>>> <https://link.getmailspring.com/link/FC05854F-A2E3-45BD-9677-A12F225F42A8@getmailspring.com/0?redirect=https%3A%2F%2Fmanual.cp2k.org%2Fcp2k-7_1-branch%2FCP2K_INPUT%2FFORCE_EVAL%2FSUBSYS%2FTOPOLOGY.html&recipient=Y3Aya0Bnb29nbGVncm91cHMuY29t>
>>> ).
>>> Best regards,
>>> Vasyl
>>> On Oct 16 2020, at 11:27 pm, sumit agrawal <sum... at gmail.com> wrote:
>>>
>>> Hii,
>>>
>>> I have recently installed cp2k in windows. I just did some exercise
>>> which is available on cp2k website. Now I want to do some bulk phase
>>> vibrational analysis. I want to make a coordinate file in which 100 water
>>> molecules and one methanol molecule is present. This methanol molecule is
>>> present in between water molecules. So how to make a coordinate file for
>>> this system.
>>>
>>> Can I use gauss view to make the coordinate file?
>>>
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