[gmx-users] problem regarding incomplete frame during gmxcheck

jaimin at iitb.ac.in jaimin at iitb.ac.in
Thu Feb 10 12:07:01 CET 2005

Dear Users,
I can run MD using the default pr.mdp file on my
protein without any problem. However,
I need a 2500 ps run and want to extract a conformation every 500 ps. For
that, I made some changes in the pr.mdp file, put it in another
directory containing the other necessary input files and ran mdrun. When
I do
tail -f pr.job, I get the following message:

Checking file pr.trr
trn version: GMX_trn_file
Last frame -1 time 0.000
WARNING: Incomplete frame: nr 0 time 0

# Atoms 68435
Last frame -1 time 0.000

Item #frames Timestep (ps)
Step 1
Time 1
Lambda 1
Coords 1
Velocities 1
Forces 1
Box 1
[guest at localhost Tub]$ tail -f pr.job
Reading file pr.tpr, VERSION 3.0.5 (single precision)
Reading file pr.tpr, VERSION 3.0.5 (single precision)
Loaded with Money

Back Off! I just backed up pr.edr to #pr.edr#
starting mdrun 'TUBULIN ALPHA CHAIN'
1250000 steps, 2500.0 ps.

step 21650, will finish at Thu Feb 17 12:39:29 2005ep 21670, will finish
at Wed step 25950, will finish at Wed Feb 16 08:22:48 2005
I have not been able to figure out the problem. I am attaching the pr.mdp
file. Please go through it and point the error.

Thanking you again,
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