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

[Travis]

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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