Anirban Ghosh wrote:
Hello Justin,
Thanks for the reply.
gmxcheck on the first trajectory shows:
-------------------------------------------------------------------------------------------------
Checking file protein_3000NS_2.trr
trn version: GMX_trn_file (single precision)
Reading frame 0 time 2957280.000
# Atoms 57296
Reading frame 1400 time 2999280.000
Item #frames Timestep (ps)
Step 1425 30
Time 1425 30
Lambda 1425 30
Coords 1425 30
Velocities 1425 30
Forces 0
Box 1425 30
---------------------------------------------------------------------------------------------------
And on the second trajectory shows:
---------------------------------------------------------------------------------------------------
Checking file B2AR_self_assembly_3500NS.trr
trn version: GMX_trn_file (single precision)
Reading frame 0 time 3000000.000
# Atoms 57296
Reading frame 16000 time 3480000.000
Item #frames Timestep (ps)
Step 16667 30
Time 16667 30
Lambda 16667 30
Coords 16667 30
Velocities 16667 30
Forces 0
Box 16667 30
---------------------------------------------------------------------------------------------------
So gmxcheck does not show any warning/error.
Then why I am getting the warning from trjcat. And how to remove it?
I don't know yet. A few more questions:
1. What version of Gromacs are you using?
2. How many total trajectories are you concatenating? You said there was a
problem from 10 -> 3000000 ns, but I don't see any times shown here below
2957280. The real problem could be early on in the trajectory.
-Justin
Thanks,
Anirban
On Thu, May 5, 2011 at 7:19 PM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
Anirban Ghosh wrote:
Hi ALL,
I am trying to use trjcat -f input files -o output_file to join
to very larger trajectories. However I am getting the following
error:
-------------------------------------------------------------------------------------------------------------------------------------------
Continue writing frames from protein_3000NS_2.trr t=2.95728e+06
ps, frame=98576 -> frame 100000 time 3000000.000 ps ->
frame 99980 time 2999400.000 ps WARNING: Frames around
t=3000000.000000 ps have a different spacing than the rest,
might be a gap or overlap that couldn't be corrected automatically.
Reading frame 0 time 3999990.000 lasttime 3e+06
Continue writing frames from protein_4000NS.trr t=3.99999e+06
ps, frame=100001
-------------------------------------------------------------------------------------------------------------------------------------------
And if I use this resultant output trajectory for further
analysis like g_sas, then a portion between around 10 ns and
3000000 ns is simply joined by a straight line.
How to remove this inconsistency from the two trajectories?
Any suggestion is welcome.
What does gmxcheck tell you about each of the individual
trajectories (prior to running trjcat)?
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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