[gmx-users] restarting mdrun

Chandan Choudhury iitdckc at gmail.com
Tue Feb 16 16:52:52 CET 2010

Hello gmxusers !!!
I want to continue my simulation, from where the point where it stopped. The
gmxcheck on .trr and cpt files are as:

$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

$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

There is a mismatch of time in both the outputs.

The date of modification of both the files as shown are:

Feb 15 19:55 state.cpt

$date -r 5-10.trr
Mon Feb 15 19:59:56 IST 2010

The cpt file shows time greater than the trr file. But the time of
modification of cpt file is less than trr file. Cannot understand the, how
to restart the mdrun. And the size of the trr file is 36GB. Can I use the
append flag in mdrun for gmx 4.0.5.

Kindly suggest.


Chandan kumar Choudhury
NCL, Pune
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