Wrong exit from RAMD runs

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Tue Apr 05 2011 - 03:11:29 CDT

Hi:
like in the past - when ramd tcl scripts were external to namd - i am
observing a wrong exit from namd runs.

With acceleration 0.1:

WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 34700
WRITING COORDINATES TO DCD FILE AT STEP 34700
WRITING COORDINATES TO RESTART FILE AT STEP 34700
FINISHED WRITING RESTART COORDINATES
The last position output (seq=34700) takes 0.019 seconds, 2907.915 MB
of memory in use
WRITING VELOCITIES TO RESTART FILE AT STEP 34700
FINISHED WRITING RESTART VELOCITIES
The last velocity output (seq=34700) takes 0.003 seconds, 2907.782 MB
of memory in use
TCL: EXIT: 34700  > MAX DISTANCE LIGAND COM - PROTEIN COM REACHED
TCL: EXIT: 34700  > LIGAND EXIT EVENT DETECTED: STOP SIMULATION
TCL: EXIT: 34700  > EXIT NAMD
Charmrun: error on request socket--
Socket closed before recv.

Actually, this has no consequences. Except for the wrong exit,
everything was in order.
*******************************
Now, however, with the same system, with acceleration 0.05:
WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 493670
WRITING COORDINATES TO RESTART FILE AT STEP 493670
FINISHED WRITING RESTART COORDINATES
The last position output (seq=493670) takes 0.014 seconds, 40916.619
MB of memory in use
WRITING VELOCITIES TO RESTART FILE AT STEP 493670
FINISHED WRITING RESTART VELOCITIES
The last velocity output (seq=493670) takes 0.004 seconds, 40916.769
MB of memory in use
Charmrun: error on request socket--
Socket closed before recv.

That is, the simulation crashed at step 493670 without the ligand
having left the protein.

In both cases, the 30 March namd night-build GNU/Linux 64 (no cuda)
Debian amd64 was used on a shared memory multi opteron machine with
huge ram. chamm force field 27, npt 1 bar, 310K. The system had been
accurately equilibrated in his solvated box, and simulation was with
ts 1 fs, rigid bonds for water only.
****************************
ATTACHED please find more detailed end of log, which I was unable to
to represent correctly in gmail plain text. There it is seen that
energies were in order. Additionally, please notice that with namd
alone (without ramd) I never had crashes with this system (same ff,
same ts = 1fs, rigid bonds water, 310K) even for longer runs.

cheers
francesco pietra


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