Re: [gmx-users] Reducing Size of Data
These step*.pdb are written when there is an instability in the system (i.e., on the verge of a crash). You can usually map them to instances in the .log file of LINCS warnings or "water molecule could not be settled" reports. -Justin Jack Shultz wrote: Hi, I am taking a look at reducing the size of my analysis. I've decreased log writing intervals. I notice mdruns generate these pdb files. Is there any way of reducing the frequency these files are written? I think that will go a long way to making my analysis easier. 05/02/2009 07:34 PM 155,211 eiwit.pdb 05/02/2009 07:43 PM 8,251,350 step117b.pdb 05/02/2009 07:44 PM 8,251,361 step117c.pdb 05/02/2009 07:38 PM 8,251,350 step20b.pdb 05/02/2009 07:38 PM 8,251,361 step20c.pdb 05/02/2009 07:38 PM 8,251,350 step27b.pdb 05/02/2009 07:38 PM 8,251,361 step27c.pdb 05/02/2009 07:40 PM 8,251,350 step79b.pdb 05/02/2009 07:40 PM 8,251,361 step79c.pdb 05/02/2009 07:40 PM 8,251,350 step80b.pdb 05/02/2009 07:41 PM 8,251,361 step80c.pdb 05/02/2009 07:41 PM 8,251,350 step91b.pdb 05/02/2009 07:41 PM 8,251,361 step91c.pdb 05/02/2009 07:41 PM 8,251,350 step92b.pdb 05/02/2009 07:42 PM 8,251,361 step92c.pdb 05/02/2009 07:42 PM 8,251,350 step93b.pdb 05/02/2009 07:42 PM 8,251,361 step93c.pdb 05/02/2009 07:42 PM 8,251,350 step94b.pdb 05/02/2009 07:42 PM 8,251,361 step94c.pdb 05/02/2009 07:42 PM 8,251,350 step96b.pdb 05/02/2009 07:43 PM 8,251,361 step96c.pdb -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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://www.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] Reducing Size of Data
Hi, I am taking a look at reducing the size of my analysis. I've decreased log writing intervals. I notice mdruns generate these pdb files. Is there any way of reducing the frequency these files are written? I think that will go a long way to making my analysis easier. 05/02/2009 07:34 PM 155,211 eiwit.pdb 05/02/2009 07:43 PM 8,251,350 step117b.pdb 05/02/2009 07:44 PM 8,251,361 step117c.pdb 05/02/2009 07:38 PM 8,251,350 step20b.pdb 05/02/2009 07:38 PM 8,251,361 step20c.pdb 05/02/2009 07:38 PM 8,251,350 step27b.pdb 05/02/2009 07:38 PM 8,251,361 step27c.pdb 05/02/2009 07:40 PM 8,251,350 step79b.pdb 05/02/2009 07:40 PM 8,251,361 step79c.pdb 05/02/2009 07:40 PM 8,251,350 step80b.pdb 05/02/2009 07:41 PM 8,251,361 step80c.pdb 05/02/2009 07:41 PM 8,251,350 step91b.pdb 05/02/2009 07:41 PM 8,251,361 step91c.pdb 05/02/2009 07:41 PM 8,251,350 step92b.pdb 05/02/2009 07:42 PM 8,251,361 step92c.pdb 05/02/2009 07:42 PM 8,251,350 step93b.pdb 05/02/2009 07:42 PM 8,251,361 step93c.pdb 05/02/2009 07:42 PM 8,251,350 step94b.pdb 05/02/2009 07:42 PM 8,251,361 step94c.pdb 05/02/2009 07:42 PM 8,251,350 step96b.pdb 05/02/2009 07:43 PM 8,251,361 step96c.pdb -- Jack http://www.facebook.com/home.php#/profile.php?id=832713248 http://hydrogenathome.org ___ gmx-users mailing listgmx-users@gromacs.org http://www.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] Reducing Size of Data
Jack Shultz wrote: Hi, I was wondering if there are any ways to reduce the amount of data produce or compact it better. On some of my runs mdruns I ran out of the default disk space BOINC allocated for my file system to run this analysis. If I use the -compact flag, does that affect the size of the trajectory files? http://wiki.gromacs.org/index.php/Using_Trajectory_Information#Reducing_Trajectory_Storage_Volume Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.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] Reducing Size of Data
Jack Shultz wrote: Hi, I was wondering if there are any ways to reduce the amount of data produce or compact it better. On some of my runs mdruns I ran out of the default disk space BOINC allocated for my file system to run this analysis. If I use the -compact flag, does that affect the size of the trajectory files? Increase nstxout, nstvout, and nstxtcout. That will reduce the size of the .trr and .xtc, which are likely the largest files that you will be writing. If you want to decrease the .xtc file even more, specify xtc_grps. If the .log and .edr files get out of hand, adjust nstlog and nstenergy. The -compact flag only affects the .log file, and is set by default. -Justin -- Justin A. Lemkul Graduate Research Assistant ICTAS Doctoral Scholar 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://www.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] Reducing Size of Data
Hi, I was wondering if there are any ways to reduce the amount of data produce or compact it better. On some of my runs mdruns I ran out of the default disk space BOINC allocated for my file system to run this analysis. If I use the -compact flag, does that affect the size of the trajectory files? -- Jack http://www.facebook.com/home.php#/profile.php?id=832713248 http://hydrogenathome.org ___ gmx-users mailing listgmx-users@gromacs.org http://www.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
