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

[sumit agrawal]

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?
>>>>>>
>>>>>> --
>>>>>> You received this message because you are subscribed to the Google
>>>>>> Groups "cp2k" group.
>>>>>> To unsubscribe from this group and stop receiving emails from it,
>>>>>> send an email to cp... at googlegroups.com
>>>>>> <https://link.getmailspring.com/link/FC05854F-A2E3-45BD-9677-A12F225F42A8@getmailspring.com/1?redirect=mailto%3Acp2k%2Bunsubscribe%40googlegroups.com&recipient=Y3Aya0Bnb29nbGVncm91cHMuY29t>
>>>>>> .
>>>>>> To view this discussion on the web visit
>>>>>> https://groups.google.com/d/msgid/cp2k/CALSDoYad_FGm4Qh5SRvZcMun3fe%3D5q1xpxeW3T5SoMcAoTH52A%40mail.gmail.com
>>>>>> <https://link.getmailspring.com/link/FC05854F-A2E3-45BD-9677-A12F225F42A8@getmailspring.com/2?redirect=https%3A%2F%2Fgroups.google.com%2Fd%2Fmsgid%2Fcp2k%2FCALSDoYad_FGm4Qh5SRvZcMun3fe%253D5q1xpxeW3T5SoMcAoTH52A%2540mail.gmail.com%3Futm_medium%3Demail%26utm_source%3Dfooter&recipient=Y3Aya0Bnb29nbGVncm91cHMuY29t>
>>>>>> .
>>>>>>
>>>>>>
>>>>>> --
>>>>>> You received this message because you are subscribed to the Google
>>>>>> Groups "cp2k" group.
>>>>>> To unsubscribe from this group and stop receiving emails from it,
>>>>>> send an email to cp... at googlegroups.com.
>>>>>> To view this discussion on the web visit
>>>>>> https://groups.google.com/d/msgid/cp2k/FC05854F-A2E3-45BD-9677-A12F225F42A8%40getmailspring.com
>>>>>> <https://groups.google.com/d/msgid/cp2k/FC05854F-A2E3-45BD-9677-A12F225F42A8%40getmailspring.com?utm_medium=email&utm_source=footer>
>>>>>> .
>>>>>>
>>>>>>
>>>>>> --
>>>>>> You received this message because you are subscribed to the Google
>>>>>> Groups "cp2k" group.
>>>>>> To unsubscribe from this group and stop receiving emails from it,
>>>>>> send an email to cp... at googlegroups.com
>>>>>> <https://link.getmailspring.com/link/E1FD0EA3-5F69-4894-B38E-7FA74A2088EE@getmailspring.com/0?redirect=mailto%3Acp2k%2Bunsubscribe%40googlegroups.com&recipient=Y3Aya0Bnb29nbGVncm91cHMuY29t>
>>>>>> .
>>>>>> To view this discussion on the web visit
>>>>>> https://groups.google.com/d/msgid/cp2k/CALSDoYaSwE%3DyxwswTkq6U5OouRZPiuev3yRJDydn%2B37kF-G4%2Bg%40mail.gmail.com
>>>>>> <https://link.getmailspring.com/link/E1FD0EA3-5F69-4894-B38E-7FA74A2088EE@getmailspring.com/1?redirect=https%3A%2F%2Fgroups.google.com%2Fd%2Fmsgid%2Fcp2k%2FCALSDoYaSwE%253DyxwswTkq6U5OouRZPiuev3yRJDydn%252B37kF-G4%252Bg%2540mail.gmail.com%3Futm_medium%3Demail%26utm_source%3Dfooter&recipient=Y3Aya0Bnb29nbGVncm91cHMuY29t>
>>>>>> .
>>>>>>
>>>>>> --
>>>>>> You received this message because you are subscribed to the Google
>>>>>> Groups "cp2k" group.
>>>>>> To unsubscribe from this group and stop receiving emails from it,
>>>>>> send an email to cp... at googlegroups.com.
>>>>>>
>>>>> To view this discussion on the web visit
>>>>>> https://groups.google.com/d/msgid/cp2k/E1FD0EA3-5F69-4894-B38E-7FA74A2088EE%40getmailspring.com
>>>>>> <https://groups.google.com/d/msgid/cp2k/E1FD0EA3-5F69-4894-B38E-7FA74A2088EE%40getmailspring.com?utm_medium=email&utm_source=footer>
>>>>>> .
>>>>>>
>>>>> --
>>>> You received this message because you are subscribed to the Google
>>>> Groups "cp2k" group.
>>>> To unsubscribe from this group and stop receiving emails from it, send
>>>> an email to cp... at googlegroups.com.
>>>>
>>> To view this discussion on the web visit
>>>> https://groups.google.com/d/msgid/cp2k/ee5fea3f-2f5c-42f2-8fb3-c6ab1042e860n%40googlegroups.com
>>>> <https://groups.google.com/d/msgid/cp2k/ee5fea3f-2f5c-42f2-8fb3-c6ab1042e860n%40googlegroups.com?utm_medium=email&utm_source=footer>
>>>> .
>>>>
>>> --
>> You received this message because you are subscribed to the Google Groups
>> "cp2k" group.
>> To unsubscribe from this group and stop receiving emails from it, send an
>> email to cp... at googlegroups.com.
>> To view this discussion on the web visit
>> https://groups.google.com/d/msgid/cp2k/24cb5e6e-ba82-45ef-be8f-90b97c9f3253n%40googlegroups.com
>> <https://groups.google.com/d/msgid/cp2k/24cb5e6e-ba82-45ef-be8f-90b97c9f3253n%40googlegroups.com?utm_medium=email&utm_source=footer>
>> .
>>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://lists.cp2k.org/archives/cp2k-user/attachments/20201019/5c7394f3/attachment.htm>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: solvprotein.pdb
Type: application/octet-stream
Size: 65194 bytes
Desc: not available
URL: <https://lists.cp2k.org/archives/cp2k-user/attachments/20201019/5c7394f3/attachment.obj>