Hi GROMACSers,
I am running into an interesting problem while propagating a long MD
trajectory for a short
peptide. I am using the checkpoint files for restart and tpbconv for
extending the trajectory length, as recommended in the on-line manual
pages. The trajectory is calculated in 100000 ps = 100 ns fragments and
ends at 4.2 microseconds due to tpbconv, with message:
"You've simulated long enough. Not writing tpr file".
Here are the details:
Things works fine for extending from 4100000 ps to 4200000 ps:
>command
tpbconv -s data/dyn41.tpr -o data/dyn42.tpr -extend 100000
>output summary
Reading toplogy and shit from data/dyn41.tpr
Reading file data/dyn41.tpr, VERSION 4.0.4 (single precision)
Writing statusfile with starting step 0 and length 2099999836
steps...
time 0.000 and length 4200000.000 ps
And this is why extension from 4200000 ps to 4300000 ps does not work:
> command
tpbconv -s data/dyn42.tpr -o data/dyn43.tpr -extend 100000
> output summary
Reading toplogy and shit from data/dyn42.tpr
Reading file data/dyn42.tpr, VERSION 4.0.4 (single precision)
Extending remaining runtime of by 100000 ps (now -2144967464 steps)
You've simulated long enough. Not writing tpr file
Apparently, the program calculates a negative total number of steps and
refuses
to continue. The possible culprit could be use of 4-byte integers - it
so happens
that 2^31 = 2147483647 and the correct total step value falls above this.
I found a message about this type of problem from 2006, suggesting use
of the "-until" option of tpbconv, but this does not solve my problem -
the outcome is the same.
I have two questions:
1) Can somebody suggest a fix or workaround for this?
2) A minor point - why is the total number of steps not a multiple of
100000/0.002 = 50000000, while the time remains in multiples of 100000 ps ?
Thanks for any ideas
Krzysztof
--
Krzysztof Kuczera
Departments of Chemistry and Molecular Biosciences
The University of Kansas
2010 Malott Hall
Lawrence, KS 66045
Tel: 785-864-5060 Fax: 785-864-5396 email: [email protected]
http://oolung.chem.ku.edu/~kuczera/home.html
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