[gmx-users] Regarding reading .gro file in python

Dilip H N cy16f01.dilip at nitk.edu.in
Thu Apr 27 21:06:02 CEST 2017


>
> 3] Yes,I want create an automatic tool in Python which sets up calculations
> for me  and possibly runs them...
> So that this Python script calls pdb2gmx, editconf, etc..
>
>
In its simplest form, that's just a bunch of system calls within the Python
script.  You can easily do this as a normal shell script without even
having to invoke Python at all.

Can u suggest me how to write it in the shell script..?? without even
having to invoke Python...


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<#>

On Fri, Apr 28, 2017 at 12:01 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 4/27/17 2:29 PM, Dilip H N wrote:
>
>> Thank you Justin Sir..
>>
>>  Yes this is what i wanted..the source code in gromacs..where is the
>> source
>> written..?? whr/in which files will i be able to get it..??
>>
>>
> Start with "get the source code" on gromacs.org and go from there.  There
> are a few developer pages online for various aspects of the source, but
> generally most programs are contained to source files named just like the
> programs; obviously there are also external functions that are shared by
> different programs, but you can easily find those with grep.
>
> -Justin
>
> Thank you
>>
>>
>>
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>> ral=cy16f01.dilip at nitk.edu.in&idSignature=22>
>> <#>
>>
>> On Thu, Apr 27, 2017 at 11:56 PM, Dilip H N <cy16f01.dilip at nitk.edu.in>
>> wrote:
>>
>> and how are the x,y,z coordinates, velocities assigned with the values..??
>>> the logic behind them in gromacs
>>>
>>> Thank you
>>>
>>>
>>>
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>>> ral=cy16f01.dilip at nitk.edu.in&idSignature=22>
>>>
>>> On Thu, Apr 27, 2017 at 11:52 PM, Dilip H N <cy16f01.dilip at nitk.edu.in>
>>> wrote:
>>>
>>> Thank you Oliver Beckstein Sir, Dawid das Sir,
>>>>
>>>> My questions are..
>>>>
>>>> 1] I got the initial configuration of a molecule in .pdb format and thn
>>>> i
>>>> gave the command
>>>> gmx editconf -f .pdb -o box.gro -c -box x y z
>>>> what happens in the background when this command is given..?? (the C++
>>>> program runs in which gromacs is written)
>>>> so what is the logic in tht program..??
>>>> 2] and i have a initial .gro file and thn i want to insert more number
>>>> of
>>>> molecules of tht to a box created i give the command
>>>> gmx insert-molecules -f .box.gro -ci ab.gro -nmol x -o abc.gro
>>>> so in the above command the molecules tht i want to insert gets inserted
>>>> in the empty spaces of the box...How is this defined in the program
>>>> (such
>>>> tht the molecules should be inserted into the empty spaces only)..??
>>>> 3] Yes,I want create an automatic tool in Python which sets up
>>>> calculations
>>>> for me  and possibly runs them...
>>>> So that this Python script calls pdb2gmx, editconf, etc..
>>>>
>>>> Thank you
>>>>
>>>>
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>>>> <https://mailtrack.io/install?source=signature&lang=en&refer
>>>> ral=cy16f01.dilip at nitk.edu.in&idSignature=22>
>>>> <#m_-6789244521733948564_m_6373284441246192622_>
>>>>
>>>>
>>>> On Thu, Apr 27, 2017 at 10:41 PM, Dawid das <addiw7 at googlemail.com>
>>>> wrote:
>>>>
>>>> Hello Dilip,
>>>>>
>>>>>  I don't really get what your problem is. What do you actually want to
>>>>> do?
>>>>> Read-in and parse a *.gro file which
>>>>> is output from MD simulation? Then for instance, your Python script
>>>>> should
>>>>> calculate something from, e.g. distance
>>>>> between centres of masses of residues of interest?
>>>>> Or do you want create an automatic tool in Python which sets up
>>>>> calculations for you and possibly runs them?
>>>>> So that this Python script calls pdb2gmx, editconf, etc.
>>>>>
>>>>> I have written various scripts for parsing output files from Gromacs
>>>>> simulations for my pretty specific purposes.
>>>>> Anyway if you may find them useful, I will be happy to share them with
>>>>> you.
>>>>>
>>>>> Best wishes,
>>>>> Dawid
>>>>>
>>>>> 2017-04-27 18:53 GMT+02:00 Oliver Beckstein <obeckste at asu.edu>:
>>>>>
>>>>> Hi Dilip,
>>>>>>
>>>>>> I think the next version of Gromacs will have some Python bindings.
>>>>>>
>>>>>> Until then you can use MDAnalysis http://mdanalysis.org : It reads
>>>>>> GRO
>>>>>> files (as well as XTC, TRR, and TPR, … and many other formats) and
>>>>>>
>>>>> loads it
>>>>>
>>>>>> into a numpy array.
>>>>>>
>>>>>> (If you have questions regarding MDAnalysis please ask on the
>>>>>>
>>>>> MDAnanlysis
>>>>>
>>>>>> user mailing http://users.mdanalysis.org list instead of the Gromacs
>>>>>> list.)
>>>>>>
>>>>>> Best wishes,
>>>>>> Oliver (disclosure: I am one of the core developers of MDAnalysis)
>>>>>>
>>>>>> On 27 Apr, 2017, at 09:46, Dilip H N <cy16f01.dilip at nitk.edu.in>
>>>>>>>
>>>>>> wrote:
>>>>>
>>>>>>
>>>>>>> Hello,
>>>>>>>
>>>>>>> I want to write a python program to read a .gro file in gromacs.. How
>>>>>>>
>>>>>> can i
>>>>>>
>>>>>>> write the program / code to read the .gro file...
>>>>>>>
>>>>>>> I need to write a python programm to read the .gro file and write as
>>>>>>>
>>>>>> it
>>>>>
>>>>>> is.. can anybody help me regarding this...
>>>>>>>
>>>>>>> Thank you..
>>>>>>>
>>>>>>> --
>>>>>>> With Best Regards,
>>>>>>>
>>>>>>> DILIP.H.N
>>>>>>> Ph.D Student
>>>>>>>
>>>>>>>
>>>>>> --
>>>>>> Oliver Beckstein, DPhil * oliver.beckstein at asu.edu
>>>>>> http://becksteinlab.physics.asu.edu/
>>>>>>
>>>>>> Assistant Professor of Physics
>>>>>> Arizona State University
>>>>>> Center for Biological Physics and Department of Physics
>>>>>> Tempe, AZ 85287-1504
>>>>>> USA
>>>>>>
>>>>>> Office: PSF 348
>>>>>> Phone: +1 (480) 727-9765
>>>>>> FAX: +1 (480) 965-4669
>>>>>>
>>>>>> Department of Physics: https://physics.asu.edu/conten
>>>>>>
>>>>> t/oliver-beckstein
>>>>>
>>>>>> Center for Biological Physics: https://cbp.asu.edu/content/
>>>>>> oliver-beckstein
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> --
>>>>>> Gromacs Users mailing list
>>>>>>
>>>>>> * Please search the archive at http://www.gromacs.org/
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>>>>>> --
>>>>> Gromacs Users mailing list
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>>>>>
>>>>
>>>>
>>>> --
>>>> With Best Regards,
>>>>
>>>> DILIP.H.N
>>>> Ph.D Student
>>>>
>>>>
>>>
>>>
>>> --
>>> With Best Regards,
>>>
>>> DILIP.H.N
>>> Ph.D Student
>>>
>>>
>>
>>
>>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
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-- 
With Best Regards,

DILIP.H.N
Ph.D Student


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