> > 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... <https://mailtrack.io/> Sent with Mailtrack <https://mailtrack.io/install?source=signature&lang=en&[email protected]&idSignature=22> <#> On Fri, Apr 28, 2017 at 12:01 AM, Justin Lemkul <[email protected]> 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 >> >> >> >> <https://mailtrack.io/> Sent with Mailtrack >> <https://mailtrack.io/install?source=signature&lang=en&refer >> [email protected]&idSignature=22> >> <#> >> >> 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 >>> >>> Thank you >>> >>> >>> >>> <https://mailtrack.io/> Sent with Mailtrack >>> <https://mailtrack.io/install?source=signature&lang=en&refer >>> [email protected]&idSignature=22> >>> >>> 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 >>>> >>>> >>>> <https://mailtrack.io/> Sent with Mailtrack >>>> <https://mailtrack.io/install?source=signature&lang=en&refer >>>> [email protected]&idSignature=22> >>>> <#m_-6789244521733948564_m_6373284441246192622_> >>>> >>>> >>>> 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 >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> -- >>>>>> Gromacs Users mailing list >>>>>> >>>>>> * Please search the archive at http://www.gromacs.org/ >>>>>> Support/Mailing_Lists/GMX-Users_List before posting! >>>>>> >>>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>>>>> >>>>>> * For (un)subscribe requests visit >>>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >>>>>> send a mail to [email protected]. >>>>>> >>>>>> -- >>>>> Gromacs Users mailing list >>>>> >>>>> * Please search the archive at http://www.gromacs.org/Support >>>>> /Mailing_Lists/GMX-Users_List before posting! >>>>> >>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>>>> >>>>> * For (un)subscribe requests visit >>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >>>>> send a mail to [email protected]. >>>>> >>>>> >>>> >>>> >>>> -- >>>> 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 > > [email protected] | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > ================================================== > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/Support > /Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to [email protected]. > -- With Best Regards, DILIP.H.N Ph.D Student -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to [email protected].
