[gmx-users] extending PMF

[Justin A. Lemkul]

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

========================================