[gmx-users] Re: Restarting mdrun

[Cuiying]

Hi,

Reply this old mail just for someone who may need the information. :)
$gmxcheck -f state.cpt
 >
 > Checking file state.cpt
 >
 > # Atoms  186864
 > Last frame         -1 time 9362.500
 >
 >
 > Item        #frames Timestep (ps)
 > Step             1
 > Time             1
 > Lambda           1
 > Coords           1
 > Velocities       1
 > Forces           0
 > Box              1
 
The time 9362.500 here indicates that the .cpt file contains the information
for the system at 9362.500 ps. If we use mdrun -s .tpr -cpi .cpt to continue
the simulation, then mdrun will read the information from .cpt file for the
system at 9362.500 ps, i.e. the simulation will begin to run from 9362.500
ps.

$gmxcheck -f 5-10.trr
 >
 > Checking file 5-10.trr
 > trn version: GMX_trn_file (single precision)
 > Reading frame       0 time 5169.500
 > # Atoms  186864
 > Reading frame    8000 time 9169.500
 >
 >
 > Item        #frames Timestep (ps)
 > Step          8395    0.5
 > Time          8395    0.5
 > Lambda        8395    0.5
 > Coords        8395    0.5
 > Velocities    8395    0.5
 > Forces           0
 > Box           8395    0.5
 
The actual simulation time that .trr file contains is from 5169.500 ps to
5169.500+8395*0.5 ps =9367 ps, i.e. .trr file contains the information for
the sytem until 9367 ps. It is actually longer than 9362.500 ps in .cpt file
since the intervals for output to .trr file and .cpt file are different.

As mentioned before, if we restart the simulaiton use .cpt file, the
simulation will begin from 9362.500 ps, i.e. the information for extra time
(from 9362.500 ps to 9367 ps) in the old .trr file will be recalculated once
the simulation is restarted.

-CY  

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