[gmx-users] restartng run..........

pavan payghan pavanapex at gmail.com
Sun Jan 10 06:08:25 CET 2010


       I want to run my system for almost 50 ns but as diskspace becomes
almost full to run system for this much time
       so which of the option u suggest
       1. Giving 10ns with each run by .mdp option .
       2.  giving full run of 50ns and then creating at each time new tpr
file to continue run for next step while storing .xtc
           at each step and concurrent removal of .trr file as it occupies a
lots of diskspace.

     While restarting run by using tpbconv to create new .tpr file for new
run may i know  following of which commond is

          1.  tpbconv -s md1_out.tpr -o md2_out.tpr -e md1_out.edr
           2  tpbconv -s md1_out.tpr -o md2_out.tpr -e md1_out.edr -extend
           tell me what -extends signifies i.e.point from where you want to
continue or extend the given number of steps.
      im asking this because when i run it using previous (1) commend i got
run in which the middle portion was
      containing no information about run.
      that is system run well till 7 ns then i killed run to continue it for
seond time this time it run well but at the end
      i found that 7ns - 13ns portin was  not there, why it is so?
     ( may it be the reason because some incomplete frames are present .)

     tell me which is the best way to check whether the system is running
well or not .?

     regarding g_rms
     While selecting groups for RMSD which is correct
     1. select whole system with solvent
      2. select only molecule of interest .
      also while choosing groups is it correct to choose both time i.e. for
least square fitting and RMSD same groups.

     Thanking you in Advance.

      Mr. Pavan Payghan
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