Re: [gmx-users] combine two gro into one
Or you can do the renumbering through feeding the file through editconf. Tom Justin A. Lemkul wrote: Sikandar Mashayak wrote: yeah I know its simple, but only concern I have is that, the index of atom/residue in two files may not be in agreement, so I have to change/shift index of atoms in one of the file. but anyway I guess I will have to do it manually That part can be done with genconf -renumber. -Justin thanks sikandar On Thu, May 13, 2010 at 10:02 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Sikandar Mashayak wrote: I need to do water channel simulations... I have two gro files with me...one for wall atoms and one for water atoms...assuming the co-ordinates of atoms are appropriate, I just need to rename the indices of each atom appropriately and append one file to anotherI plan to do it by hand...but it will be great if there is an automatic way of doing it in gromacs? This is a simple task that can be done with the Unix 'cat' command. Thus there is no Gromacs tool that reproduces this function. A few seconds with a text editor after concatenation to remove unnecessary title lines and box vectors and you're done, assuming (as you've said) that all the coordinates are appropriately defined. The whole process probably takes less typing than sending this email :) -Justin thanks sikandar -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] combine two gro into one
I need to do water channel simulations... I have two gro files with me...one for wall atoms and one for water atoms...assuming the co-ordinates of atoms are appropriate, I just need to rename the indices of each atom appropriately and append one file to anotherI plan to do it by hand...but it will be great if there is an automatic way of doing it in gromacs? thanks sikandar -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] combine two gro into one
Sikandar Mashayak wrote: I need to do water channel simulations... I have two gro files with me...one for wall atoms and one for water atoms...assuming the co-ordinates of atoms are appropriate, I just need to rename the indices of each atom appropriately and append one file to anotherI plan to do it by hand...but it will be great if there is an automatic way of doing it in gromacs? This is a simple task that can be done with the Unix 'cat' command. Thus there is no Gromacs tool that reproduces this function. A few seconds with a text editor after concatenation to remove unnecessary title lines and box vectors and you're done, assuming (as you've said) that all the coordinates are appropriately defined. The whole process probably takes less typing than sending this email :) -Justin thanks sikandar -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] combine two gro into one
yeah I know its simple, but only concern I have is that, the index of atom/residue in two files may not be in agreement, so I have to change/shift index of atoms in one of the file. but anyway I guess I will have to do it manually thanks sikandar On Thu, May 13, 2010 at 10:02 PM, Justin A. Lemkul jalem...@vt.edu wrote: Sikandar Mashayak wrote: I need to do water channel simulations... I have two gro files with me...one for wall atoms and one for water atoms...assuming the co-ordinates of atoms are appropriate, I just need to rename the indices of each atom appropriately and append one file to anotherI plan to do it by hand...but it will be great if there is an automatic way of doing it in gromacs? This is a simple task that can be done with the Unix 'cat' command. Thus there is no Gromacs tool that reproduces this function. A few seconds with a text editor after concatenation to remove unnecessary title lines and box vectors and you're done, assuming (as you've said) that all the coordinates are appropriately defined. The whole process probably takes less typing than sending this email :) -Justin thanks sikandar -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] combine two gro into one
Sikandar Mashayak wrote: yeah I know its simple, but only concern I have is that, the index of atom/residue in two files may not be in agreement, so I have to change/shift index of atoms in one of the file. but anyway I guess I will have to do it manually That part can be done with genconf -renumber. -Justin thanks sikandar On Thu, May 13, 2010 at 10:02 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Sikandar Mashayak wrote: I need to do water channel simulations... I have two gro files with me...one for wall atoms and one for water atoms...assuming the co-ordinates of atoms are appropriate, I just need to rename the indices of each atom appropriately and append one file to anotherI plan to do it by hand...but it will be great if there is an automatic way of doing it in gromacs? This is a simple task that can be done with the Unix 'cat' command. Thus there is no Gromacs tool that reproduces this function. A few seconds with a text editor after concatenation to remove unnecessary title lines and box vectors and you're done, assuming (as you've said) that all the coordinates are appropriately defined. The whole process probably takes less typing than sending this email :) -Justin thanks sikandar -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
