[gmx-users] Time frames missing

Sun Iba sun.iba2 at gmail.com
Mon Aug 1 08:41:30 CEST 2016

Hello everyone

I have extended a 100 ns simulation of a protein in water up to 200 ns.
However, the system kept shutting down during the course of simulation and
i had to restart the runs twice. Following are the files I obtained after
completion of mdrun (I am writing information of .xtc only, for .trr its

*md_0_1.xtc = 0 to 100 ns*

*new.xtc = 99.990 to 159.990*

*v.xtc = 166.050 to 179.050*
*traj-comp.xtc = 179.620 to 200.00 ns*

Now I am surprised to see that the time frames from 159.990 to 166.050 are
not written to any file. I have also checked the .trr and .xtc file with
gmx check and found that time frames are incomplete after the follwoing

 gmx check -f new.trr

Checking file new.trr
trn version: GMX_trn_file (single precision)
Reading frame       0 time 99990.000
# Atoms  133688
Reading frame    6000 time 159990.000

*WARNING: Incomplete frame: nr 6607 time 166060*

Item        #frames Timestep (ps)
Step          6607    10
Time          6607    10
Lambda        6607    10
Coords        6607    10
Velocities    6607    10
Forces           0
Box           6607    10

Now I am not sure to catenate the avaialble file or should i start the run
again from 159.990 to 166.050? iF YES, WHAT WOULD BE THE COMMAND FOR THAT...

With Regards

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