Dear Mark, That was a great deal of help. This time, I agree with your last sentence ;-) Thanks a lot!
Cheers, Mah On Wed, Jan 28, 2015 at 2:23 PM, mah maz <mahma...@gmail.com> wrote: > 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.
