[CP2K-user] [CP2K:14088] How to make coordinate file

[Lucas Lodeiro]

Hi,

You have to make pdb files for each molecule that you need to put in a box
via packmol. If you can make a water-protein cell, the water-N2 cell is the
same, just change the protein.pdb file to N2.pdb and rum packmol.
Here are some useful examples to make differents types of boxes and
interfaces: http://m3g.iqm.unicamp.br/packmol/examples.shtml

El lun., 19 oct. 2020 a las 8:02, sumit agrawal (<sumitag... at gmail.com>)
escribió:

> Hii,
>
> I tried to make a protein, containing a solvation cell via packmol. Here
> the solvation cell is water. Now I want to change the solvation cell. I
> want a N2 molecule, containing a solvation cell. How to do it via packmol?
> Since in packmol only water pdb file is available.
>
> I am attaching a input file of a protein, containing water molecules.
>
>
>
> On Sat, Oct 17, 2020 at 8:57 AM sumit agrawal <sumitag... at gmail.com>
> wrote:
>
>> 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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