Re: [gmx-users] coordinates file format
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 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 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 z4 >> 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 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 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: tx1 y1 z1 x2 y2 z2 02.4 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 wrote: > Dear all, > > I have extracted a file of coordinates after a simulation with 100 > 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.
Re: [gmx-users] coordinates file format
On Wed, Jan 28, 2015 at 11:53 AM, mah maz wrote: > Dear Mark, Erik > > Mark, thank you very much! I asked google and it didn't know either! ;-) > Sure it does. https://www.google.com/search?q=libxdrfile. You'd have to work out how to call its C functions from FORTRAN, though. your code also didn't work in FORTRAN. Of course... I did call it pseudocode... 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. > Reading fixed-width fields from an .xvg file like that written by g_traj -ox is the only I/O thing FORTRAN77 can do reasonably, so if that's the only skill set you have available, you'll need to learn how to use FORMAT and friends :-) Meanwhile, your competitors wrote their code in Python 15 times quicker and published another paper ;-) Mark > Regards, > Mah > > On Tue, Jan 27, 2015 at 12:31 PM, mah maz 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 z4 > > 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 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 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: > >>> tx1 y1 z1 x2 y2 z2 > >>> 02.4 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 wrote: > >>> > Dear all, > > I have extracted a file of coordinates after a simulation with 100 > 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. > -- 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.
Re: [gmx-users] coordinates file format
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 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 z4 > 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 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 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: >>> tx1 y1 z1 x2 y2 z2 >>> 02.4 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 wrote: >>> Dear all, I have extracted a file of coordinates after a simulation with 100 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.
Re: [gmx-users] coordinates file format
On Tue, Jan 27, 2015 at 10:01 AM, mah maz wrote: > Dear Justin and Mark, > > I think you are both right. > > I didn't get your last sentence Mark! What is a libxdrfile? > Ask google ;-) It's a library distributed from the GROMACS website to make it easier to read files into C and (particularly) Fortran programs. > 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 z4 > completely difficult and confusing for me and the program both! > The following pseudocode reads both, because they're the same thing! ignore_useless_title_row_if_present() for frame (1 .. end of file) frametime[frame] = read_next_number() for atom (1 .. number_of_atoms) for dim (x y z) framecoords[atom][dim] = read_next_number() The field widths are fixed, so this probably even works in Fortran. According to your points, I can come to the conclusion that changing the > file format is not possible. > It's perfectly possible to write a script to transform it to whatever you like. But that would serve no useful purpose. Mark > I appreciate your help as usual. thanks alot! > > Cheers, > Mah > > > > > > > > On Mon, Jan 26, 2015 at 8:01 PM, mah maz 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 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: > >> tx1 y1 z1 x2 y2 z2 > >> 02.4 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 wrote: > >> > >>> Dear all, > >>> > >>> I have extracted a file of coordinates after a simulation with 100 > >>> 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. > -- 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.
Re: [gmx-users] coordinates file format
On 27 Jan 2015, at 09:01, mah maz mailto:mahma...@gmail.com>> wrote: 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 z4 completely difficult and confusing for me and the program both! So if I get this right you want to change the spacing between xn yn zn and xn+1 yn+1 zn+1. It will take you 5 min to write a python script to do that. And I can’t see why the current output format would be “confusing” for a program. Kind regards, Erik Erik Marklund, PhD Postdoctoral Research Fellow, Fulford JRF Department of Chemistry Physical & Theoretical Chemistry Laboratory University of Oxford South Parks Road Oxford OX1 3QZ -- 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.
Re: [gmx-users] coordinates file format
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 z4 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 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 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: >> tx1 y1 z1 x2 y2 z2 >> 02.4 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 wrote: >> >>> Dear all, >>> >>> I have extracted a file of coordinates after a simulation with 100 >>> 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.
Re: [gmx-users] coordinates file format
On Mon, Jan 26, 2015 at 5:31 PM, mah maz 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. What do you mean by "they?" Every atom has three adjacent columns and each of the dimensions has its own column. Your example of a preferred format did this also. > Can I do anything to a > result file to be in my preferable format? > The only difference in your preference seems to be extra whitespace between triples of columns corresponding to atoms. This is basically unnecessary for doing parsing - you already know that the columns are in triples of xyz. You could insert the extra whitespace yourself with your scripting language of choice, but the only advantage of that might be if you then plan to read the format into a Fortran program, in which case you deserve pain for not using libxdrfile to read the original trajectory ;-) Cheers, Mark > Many Thanks! > Regards, > Mah > > On Mon, Jan 26, 2015 at 12:08 PM, mah maz 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: > > tx1 y1 z1 x2 y2 z2 > > 02.4 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 wrote: > > > >> Dear all, > >> > >> I have extracted a file of coordinates after a simulation with 100 > >> 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. > -- 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.
Re: [gmx-users] coordinates file format
On 1/26/15 11:31 AM, mah maz 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? Which sort of format would you prefer? You say the coordinates are not in a "special format," but in fact they are in a completely predictable format, which you have identified - (x,y,z) for every atom in the selection. The output is indeed cumbersome (it is a bit of a number dump), but it is easily parsed with any scripting language because the order is known. The file may not be aesthetically pleasing, but it's perfectly functional. -Justin Many Thanks! Regards, Mah On Mon, Jan 26, 2015 at 12:08 PM, mah maz 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: tx1 y1 z1 x2 y2 z2 02.4 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 wrote: Dear all, I have extracted a file of coordinates after a simulation with 100 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! -- == 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 jalem...@outerbanks.umaryland.edu | (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 gmx-users-requ...@gromacs.org.
Re: [gmx-users] coordinates file format
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 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: > tx1 y1 z1 x2 y2 z2 > 02.4 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 wrote: > >> Dear all, >> >> I have extracted a file of coordinates after a simulation with 100 >> 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.
Re: [gmx-users] coordinates file format
On Mon, Jan 26, 2015 at 9:38 AM, mah maz 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: > tx1 y1 z1 x2 y2 z2 > 02.4 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? > I don't understand. That is already the format of gmx traj -ox. You can see that in the XVG legend. Re-grouping by atom number is straightforward to do while you read it into whatever you plan to use next. Mark > thank you! > > On Mon, Jan 26, 2015 at 11:54 AM, mah maz wrote: > > > Dear all, > > > > I have extracted a file of coordinates after a simulation with 100 > > 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. > -- 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.
Re: [gmx-users] coordinates file format
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: tx1 y1 z1 x2 y2 z2 02.4 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 wrote: > Dear all, > > I have extracted a file of coordinates after a simulation with 100 > 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.
Re: [gmx-users] coordinates file format
Hi, What do you mean by "classified," and what do you want to do with them? Mark On Mon, Jan 26, 2015 at 9:24 AM, mah maz wrote: > Dear all, > > I have extracted a file of coordinates after a simulation with 100 > 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. > -- 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.
