[CP2K-user] [CP2K:14090] How to make coordinate file

[sumit agrawal]

Thank you... It's really helpful.

On Mon, 19 Oct, 2020, 9:47 pm Lucas Lodeiro, <eluni... at gmail.com> wrote:

> 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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