[CP2K-user] [CP2K:14073] How to make coordinate file

[Vasyl Stotskyi]

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 ?
>
>
> On Fri, Oct 16, 2020 at 9:04 AM Vasyl Stotskyi <vasyl.... at gmail.com (mailto: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 (mailto: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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