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&[email protected]&idSignature=22> <#> 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/content/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 -- 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].
