Re: [gmx-users] box vectors - regd
Dear Mark, Once again I am very thankful to you for your reply, I have extracted box vectors from .XTC file by using g_traj with -ob option with this I was able to get only six vector components viz XX YY ZZ YX ZX and ZY only how about remaining three vector components XY XZ and YZ . I have used triclinic box for my simulations I know that XY XZ and YZ will be zero, moreover I have used pcoupltype = anisotropic with compressibility values as compressibility = 4.5e-5 4.5e-5 4.5e-5 0.0 0.0 0.0 in my .mdp file. Here my question is why I am not getting XY XZ and YZ components in my output file though they might be zero. Is this because of above specified .mdp options or something else ? Can you please let me know what might be the probable reason ? Thank you in advance. On Thu, Aug 16, 2012 at 11:17 AM, Mark Abraham mark.abra...@anu.edu.au wrote: On 16/08/2012 3:22 PM, ramesh cheerla wrote: Dear Mark, Thank you for your reply, as you suggested I will go through the sec 7.4 and 8 of the manual and moreover how would I get exact box vectors XX YY ZZ XY XZ YX YZ ZX ZY for each frame of trajectory in gromacs They're in the trajectory file with each frame. As I am new to gromacs I have no Idea where these will be stored ( other than gro file ). In NAMD .XTC file contains box vectors for each step of the simulation like this is there any file in gromacs that stores these box vectors for each step, Same. if so how can i extract them. Probably however you did so with NAMD, or with g_traj or gmxdump. Mark Please suggest me a way. Thank you. On Thu, Aug 16, 2012 at 4:52 AM, Mark Abraham mark.abra...@anu.edu.au wrote: On 16/08/2012 5:46 AM, ramesh cheerla wrote: Dear Gromacs users, I am using gromacs for simulations of a polymer, for that I am planing to see how lattice parameters a , b c are varying during simulation. Here lattice parameter a is the length of unit cell along X- direction, b is the length of the unit cell along Y axis and c is along Z -axis. For my polymer polymer chains are not exactly oriented along Z- direction they are a little bit tilted from the Z- axis. a and b are along x and Y directions respectively so that I can get lattice parameters a and b just by dividing box lengths along those directions with the number of unit cells in those directions. As the c- direction and Z- direction are not exactly same ( c is a little bit tilted from Z ) in this case I shouldn't divide the box length along Z - direction with the number of unit cells in that direction to get lattice parameter c. Here my questions are: 1) How can I calculate exact C lattice parameter from simulation data ? is there any way to get appropriate c? 2) How one can get box vectors XX YY ZZ XY XZ YX YZ ZX and ZY for total trajectory, as g_energy is giving only Box - X , Box-Y and Box- Z but i need exact box vectors for valid lattice parameters calculations. Sounds like g_energy is reminding you that you had a rectilinear simulation cell when you started, and still do. There are various ways to measure angles that will help you address your problem, if you check out manual sections 7.4 and 8. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] box vectors - regd
Dear Gromacs users, I am using gromacs for simulations of a polymer, for that I am planing to see how lattice parameters a , b c are varying during simulation. Here lattice parameter a is the length of unit cell along X- direction, b is the length of the unit cell along Y axis and c is along Z -axis. For my polymer polymer chains are not exactly oriented along Z- direction they are a little bit tilted from the Z- axis. a and b are along x and Y directions respectively so that I can get lattice parameters a and b just by dividing box lengths along those directions with the number of unit cells in those directions. As the c- direction and Z- direction are not exactly same ( c is a little bit tilted from Z ) in this case I shouldn't divide the box length along Z - direction with the number of unit cells in that direction to get lattice parameter c. Here my questions are: 1) How can I calculate exact C lattice parameter from simulation data ? is there any way to get appropriate c? 2) How one can get box vectors XX YY ZZ XY XZ YX YZ ZX and ZY for total trajectory, as g_energy is giving only Box - X , Box-Y and Box- Z but i need exact box vectors for valid lattice parameters calculations. Any help will be highly appreciated. Thank you in advance. Regards, Ramesh. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] box vectors - regd
On 16/08/2012 5:46 AM, ramesh cheerla wrote: Dear Gromacs users, I am using gromacs for simulations of a polymer, for that I am planing to see how lattice parameters a , b c are varying during simulation. Here lattice parameter a is the length of unit cell along X- direction, b is the length of the unit cell along Y axis and c is along Z -axis. For my polymer polymer chains are not exactly oriented along Z- direction they are a little bit tilted from the Z- axis. a and b are along x and Y directions respectively so that I can get lattice parameters a and b just by dividing box lengths along those directions with the number of unit cells in those directions. As the c- direction and Z- direction are not exactly same ( c is a little bit tilted from Z ) in this case I shouldn't divide the box length along Z - direction with the number of unit cells in that direction to get lattice parameter c. Here my questions are: 1) How can I calculate exact C lattice parameter from simulation data ? is there any way to get appropriate c? 2) How one can get box vectors XX YY ZZ XY XZ YX YZ ZX and ZY for total trajectory, as g_energy is giving only Box - X , Box-Y and Box- Z but i need exact box vectors for valid lattice parameters calculations. Sounds like g_energy is reminding you that you had a rectilinear simulation cell when you started, and still do. There are various ways to measure angles that will help you address your problem, if you check out manual sections 7.4 and 8. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] box vectors - regd
Dear Mark, Thank you for your reply, as you suggested I will go through the sec 7.4 and 8 of the manual and moreover how would I get exact box vectors XX YY ZZ XY XZ YX YZ ZX ZY for each frame of trajectory in gromacs As I am new to gromacs I have no Idea where these will be stored ( other than gro file ). In NAMD .XTC file contains box vectors for each step of the simulation like this is there any file in gromacs that stores these box vectors for each step, if so how can i extract them. Please suggest me a way. Thank you. On Thu, Aug 16, 2012 at 4:52 AM, Mark Abraham mark.abra...@anu.edu.au wrote: On 16/08/2012 5:46 AM, ramesh cheerla wrote: Dear Gromacs users, I am using gromacs for simulations of a polymer, for that I am planing to see how lattice parameters a , b c are varying during simulation. Here lattice parameter a is the length of unit cell along X- direction, b is the length of the unit cell along Y axis and c is along Z -axis. For my polymer polymer chains are not exactly oriented along Z- direction they are a little bit tilted from the Z- axis. a and b are along x and Y directions respectively so that I can get lattice parameters a and b just by dividing box lengths along those directions with the number of unit cells in those directions. As the c- direction and Z- direction are not exactly same ( c is a little bit tilted from Z ) in this case I shouldn't divide the box length along Z - direction with the number of unit cells in that direction to get lattice parameter c. Here my questions are: 1) How can I calculate exact C lattice parameter from simulation data ? is there any way to get appropriate c? 2) How one can get box vectors XX YY ZZ XY XZ YX YZ ZX and ZY for total trajectory, as g_energy is giving only Box - X , Box-Y and Box- Z but i need exact box vectors for valid lattice parameters calculations. Sounds like g_energy is reminding you that you had a rectilinear simulation cell when you started, and still do. There are various ways to measure angles that will help you address your problem, if you check out manual sections 7.4 and 8. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] box vectors - regd
On 16/08/2012 3:22 PM, ramesh cheerla wrote: Dear Mark, Thank you for your reply, as you suggested I will go through the sec 7.4 and 8 of the manual and moreover how would I get exact box vectors XX YY ZZ XY XZ YX YZ ZX ZY for each frame of trajectory in gromacs They're in the trajectory file with each frame. As I am new to gromacs I have no Idea where these will be stored ( other than gro file ). In NAMD .XTC file contains box vectors for each step of the simulation like this is there any file in gromacs that stores these box vectors for each step, Same. if so how can i extract them. Probably however you did so with NAMD, or with g_traj or gmxdump. Mark Please suggest me a way. Thank you. On Thu, Aug 16, 2012 at 4:52 AM, Mark Abraham mark.abra...@anu.edu.au wrote: On 16/08/2012 5:46 AM, ramesh cheerla wrote: Dear Gromacs users, I am using gromacs for simulations of a polymer, for that I am planing to see how lattice parameters a , b c are varying during simulation. Here lattice parameter a is the length of unit cell along X- direction, b is the length of the unit cell along Y axis and c is along Z -axis. For my polymer polymer chains are not exactly oriented along Z- direction they are a little bit tilted from the Z- axis. a and b are along x and Y directions respectively so that I can get lattice parameters a and b just by dividing box lengths along those directions with the number of unit cells in those directions. As the c- direction and Z- direction are not exactly same ( c is a little bit tilted from Z ) in this case I shouldn't divide the box length along Z - direction with the number of unit cells in that direction to get lattice parameter c. Here my questions are: 1) How can I calculate exact C lattice parameter from simulation data ? is there any way to get appropriate c? 2) How one can get box vectors XX YY ZZ XY XZ YX YZ ZX and ZY for total trajectory, as g_energy is giving only Box - X , Box-Y and Box- Z but i need exact box vectors for valid lattice parameters calculations. Sounds like g_energy is reminding you that you had a rectilinear simulation cell when you started, and still do. There are various ways to measure angles that will help you address your problem, if you check out manual sections 7.4 and 8. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
