[CP2K-user] [CP2K:14074] How to make coordinate file

[Lucas Lodeiro]

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 (<vasyl.... 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 <sumitag... 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 <vasyl.... 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 <sumitag... 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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