[CP2K-user] [CP2K:14080] How to make coordinate file

[sumit agrawal]

Okay....Thanks a lot!!!

On Sat, Oct 17, 2020 at 1:25 AM Travis <polla... at gmail.com> wrote:

> Hi,
>
> Packmol simply packs a box of some size with a randomized geometry. There
> will likely be overlapping atoms and other bad contacts. You'll need to *at
> least* optimize it but preferably equilibrate the liquid structure with a
> reasonable force field before using it with CP2K.
>
> -T
>
> On Saturday, October 17, 2020 at 2:57:32 AM UTC-4 sum... at gmail.com
> wrote:
>
>> 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 <po... 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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