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
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On Thu, Apr 27, 2017 at 11:56 PM, Dilip H N <[email protected]>
wrote:
and how are the x,y,z coordinates, velocities assigned with the values..??
the logic behind them in gromacs
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On Thu, Apr 27, 2017 at 11:52 PM, Dilip H N <[email protected]>
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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On Thu, Apr 27, 2017 at 10:41 PM, Dawid das <[email protected]>
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 <[email protected]>:
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 <[email protected]>
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 * [email protected]
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
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With Best Regards,
DILIP.H.N
Ph.D Student
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With Best Regards,
DILIP.H.N
Ph.D Student
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==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
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University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
[email protected] | (410) 706-7441
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