Rebeca García Fandiño wrote:
Hello,
I am trying to extend a PMF calculation (Umbrella Sampling calculation).
In first place I used tpbconv:
tpbconv -s umbrella_3.tpr -o umbrella_3b.tpr -extend 1000
And then I run it using mdrun:
mdrun -s umbrella_3b.tpr -cpi umbrella_3.cpt -pf pullf-umbrella_3.xvg
-px pullx-umbrella_3.xvg -append
I got the following error:
.....................................
(...)
Reading file umbrella_3b.tpr, VERSION 4.0.7 (single precision)
Reading checkpoint file umbrella_3.cpt generated: Fri Jul 1 00:18:26
2011tpbconv -s umbrella_3.tpr -o umbrella_3b.tpr -extend 1000
-------------------------------------------------------
Program mdrun, VERSION 4.0.7
Source code file: checkpoint.c, line: 1261
Fatal error:
Truncation of file umbrella_3.trr failed.
-------------------------------------------------------
"set: No match." (tcsh)
Error on node 0, will try to stop all the nodes
Halting parallel program mdrun on CPU 0 out of 8
gcq#269: "set: No match." (tcsh)
.......................................
Do I need the *trr files for extending the simulation. In a normal
calculation, the *cpt is enough for extending a simulation. Is any
difference for the PMF calculations?
If you are appending, then all files must be present in the working directory so
that they can be appended to. If you have deleted, moved, or renamed the files,
the appending will fail.
-Justin
Thanks a lot in advance.
Best wishes,
Dr. Rebeca Garcia
Santiago de Compostela University
Spain
--
========================================
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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