Re: [gmx-users] scripting question
I would highly recommend you to learn some language like Python or Ruby and use it for this kind of stuff. More flexible and more maintainable than shell scripting, and not harder. cheers, m. On 16/07/10 12:03, Hassan Shallal wrote: Thanks alot Rui for the hint From: gmx-users-boun...@gromacs.org on behalf of J. Rui Rodrigues Sent: Fri 7/16/2010 3:26 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] scripting question google: for loop bash On Fri, 16 Jul 2010 02:57:12 -0700, Hassan Shallal wrote Dear Gromacs users, This question is much more of a unix/linux scripting issue. Let's say I have 10 pdb files named mt_1.pdb, mt_2.pdb, .mt_10.pdb. If I need to energy minimize the 10 pdb files using the same em.mdp and the same mt.top file, how can I create a script for minimizing the 10 files without me specifying each file for grommp and mdrun on an individual basis, for 10 files it could be fine, but for more files like 100 or 200, this is quite time consuming and liable for errors? Any help of hint is very appreciated Hassan -- Webmail ESTG de Leiria (http://webmail.estg.ipleiria.pthttp://webmail.estg.ipleiria.pt/ ) -- 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] scripting question
google: for loop bash On Fri, 16 Jul 2010 02:57:12 -0700, Hassan Shallal wrote Dear Gromacs users, This question is much more of a unix/linux scripting issue. Let's say I have 10 pdb files named mt_1.pdb, mt_2.pdb, .mt_10.pdb. If I need to energy minimize the 10 pdb files using the same em.mdp and the same mt.top file, how can I create a script for minimizing the 10 files without me specifying each file for grommp and mdrun on an individual basis, for 10 files it could be fine, but for more files like 100 or 200, this is quite time consuming and liable for errors? Any help of hint is very appreciated Hassan -- Webmail ESTG de Leiria (http://webmail.estg.ipleiria.pt) -- 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] scripting question
Thanks alot Rui for the hint From: gmx-users-boun...@gromacs.org on behalf of J. Rui Rodrigues Sent: Fri 7/16/2010 3:26 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] scripting question google: for loop bash On Fri, 16 Jul 2010 02:57:12 -0700, Hassan Shallal wrote Dear Gromacs users, This question is much more of a unix/linux scripting issue. Let's say I have 10 pdb files named mt_1.pdb, mt_2.pdb, .mt_10.pdb. If I need to energy minimize the 10 pdb files using the same em.mdp and the same mt.top file, how can I create a script for minimizing the 10 files without me specifying each file for grommp and mdrun on an individual basis, for 10 files it could be fine, but for more files like 100 or 200, this is quite time consuming and liable for errors? Any help of hint is very appreciated Hassan -- Webmail ESTG de Leiria (http://webmail.estg.ipleiria.pt http://webmail.estg.ipleiria.pt/ ) -- 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 winmail.dat-- 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
