From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Tue Feb 18 2014 - 05:44:34 CST
In a t-remd with a 41 aa peptide, 32 replicas, restarting t-remd does not
keep trace of the status of colvars (rmsd applied to a small, initial
stretch of the peptide), as I posted before for GB t-remd.
Now, for the same t-remd, in a periodic box with TIP3 water, on restarting
the initial, correct t-remd, the status of the cell is incorrectly
reported in the .xsc file for replicas 20, 22, 23, and 25, with crash
>From the .err file (or the signle log files in the various replicas)
Reason: REPLICA 23 FATAL ERROR: PMEGridSizeX 70 is too small for cell
length 73.054500 and PMEGridSpacing 1.000000
namd2: machine.c:708: LrtsAbort: Assertion `0' failed.
------------- Processor 0 Exiting: Called CmiAbort ------------
Reason: REPLICA 22 FATAL ERROR: PMEGridSizeX 70 is too small for cell
length 72.344600 and PMEGridSpacing 1.000000
namd2: machine.c:708: LrtsAbort: Assertion `0' failed.
------------- Processor 0 Exiting: Called CmiAbort ------------
Reason: REPLICA 20 FATAL ERROR: PMEGridSizeX 70 is too small for cell
length 70.826300 and PMEGridSpacing 1.000000
------------- Processor 0 Exiting: Called CmiAbort ------------
Reason: REPLICA 25 FATAL ERROR: PMEGridSizeX 70 is too small for cell
length 74.891500 and PMEGridSpacing 1.000000
Actually, the same can be expected for all replicas, as the other replicas
had not yet reached the stage of looking for .xsc (same problem observed in
GB for the status of colvars)
No such problems with the same files for MD in explicit water: both the
cell status and the status of colvars are correctly transferred to the
restarting MD.
francesco pietra
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