[gmx-users] "simulated long enough" message from tpbconv

Krzysztof Kuczera kkuczera at ku.edu
Fri Jul 23 22:40:47 CEST 2010


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:
 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 
                                 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 
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 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: kkuczera at ku.edu

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