Dear Mark, Erik Mark, thank you very much! I asked google and it didn't know either! ;-) your code also didn't work in FORTRAN. I've searched and found out it is not probably an easy task to read a .trr file and even .xtc in FORTRAN. Have you got any other ideas? Erik, It took me more than 5hrs to read it in FORTRAN and I couldn't succeed! I'm not familiar with python. thanks anyway. Regards, Mah
On Tue, Jan 27, 2015 at 12:31 PM, mah maz <mahma...@gmail.com> wrote: > Dear Justin and Mark, > > I think you are both right. > > I didn't get your last sentence Mark! What is a libxdrfile? > > Justin, The problem is I have so many atoms in the system. As I said the > best format for reading data is to be like this: > time x1 y1 z1 x2 y2 z2 ....... xn yn zn > 0 1 2 3 2 3 4 8 5 6 > 0.1 > 0.2 > ... > as you know the trajectory format is like this: > > (t=)0 x1 y1 z1 x2 y2 z2 x3 y3 z3 x4 y4 z4....... > x5 y5 z5 ......... x4000 y4000 z4000 > (t=)0.1 x1 y1 z1 x2 y2 z2.............. > x5 y5 z5 ....... x4000 y4000 z40000 > completely difficult and confusing for me and the program both! > > According to your points, I can come to the conclusion that changing the > file format is not possible. > I appreciate your help as usual. thanks alot! > > Cheers, > Mah > > > > > > > > On Mon, Jan 26, 2015 at 8:01 PM, mah maz <mahma...@gmail.com> wrote: > >> Dear Mark, >> >> Thanks for your reply. I think it is not! I have 4000 atoms, the first >> number is time, then 4000 x y and z: x1,y1,z1, x2, y2, z2, ....,x4000, >> y4000, z4000. They are following each other not in a special order. Then >> the next time step starts with x1,y1,z1,....,x4000, y4000, z4000. So, they >> are not in a column as they are supposed to be. Can I do anything to a >> result file to be in my preferable format? >> >> Many Thanks! >> Regards, >> Mah >> >> On Mon, Jan 26, 2015 at 12:08 PM, mah maz <mahma...@gmail.com> wrote: >> >>> Hi Mark, >>> I want to have X Y Z of each atom for all time step apart from other >>> atoms so that I can use them as data for programing; like this for instance: >>> t x1 y1 z1 x2 y2 z2 >>> 0 2.4 3.5 4.5 5.6 7.9 9.8 >>> 0.1 5.5 6.7 8.9 >>> ... >>> in which 0 and 0.1 are time and the rest are x1 y1 z1 of the 1st atom >>> and x2 y2 z2 are for the 2nd atom. >>> Is it possible to get the file in a desired format? >>> thank you! >>> >>> On Mon, Jan 26, 2015 at 11:54 AM, mah maz <mahma...@gmail.com> wrote: >>> >>>> Dear all, >>>> >>>> I have extracted a file of coordinates after a simulation with 1000000 >>>> steps writen every 1000 steps, by "g_traj -s -ox" . The result is a file in >>>> which the first column is time and all coordinates are following it. Is >>>> there a way that I can get coordinates of each time step in a more >>>> classified way? >>>> >>>> Thanks! >>>> >>> >>> >> > -- 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 gmx-users-requ...@gromacs.org.