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

[Travis]

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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