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