Re: Fwd: Wrong exit from RAMD runs

From: Jim Phillips (jim_at_ks.uiuc.edu)
Date: Wed Apr 13 2011 - 09:59:25 CDT

RAMD uses a rather unconventional approach to exiting the program:

  #***** Terminate NAMD if the ligand has exited from the protein
  if { $exitFlag == 1 } {
   print "EXIT: $timeStep > MAX DISTANCE LIGAND COM - PROTEIN COM REACHED"
   print "EXIT: $timeStep > LIGAND EXIT EVENT DETECTED: STOP SIMULATION"
   print "EXIT: $timeStep > EXIT NAMD"
   set process [pid]
   exec kill -9 $process
  }

Changing "exec kill -9 $process" to simply "exit" will exit cleanly.

-Jim

On Tue, 5 Apr 2011, Francesco Pietra wrote:

> This is to add that now, for the first time out of so many runs in the
> past and present, I have seen a formally correct exit from a ramd run.
> Same system as the wrong exit described below. The only difference was
> the acceleration.
> ENERGY:  196500       935.6674      1456.8738       592.0131
> 99.5454        -124940.0012     10232.3179         0.0000
> 0.0000     21324.5279         -90299.0557       309.2950
> -111623.5835    -90268.0435       309.4156           -144.5299
> 147.9136    331258.5733       141.8714       139.1275
>
> WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 196500
> WRITING COORDINATES TO DCD FILE AT STEP 196500
> WRITING COORDINATES TO RESTART FILE AT STEP 196500
> FINISHED WRITING RESTART COORDINATES
> The last position output (seq=196500) takes 0.021 seconds, 16315.520
> MB of memory in use
> WRITING VELOCITIES TO RESTART FILE AT STEP 196500
> FINISHED WRITING RESTART VELOCITIES
> The last velocity output (seq=196500) takes 0.004 seconds, 16315.262
> MB of memory in use
> TCL: EXIT: 196500  > MAX DISTANCE LIGAND COM - PROTEIN COM REACHED
> TCL: EXIT: 196500  > LIGAND EXIT EVENT DETECTED: STOP SIMULATION
> TCL: EXIT: 196500  > EXIT NAMD
>
>
> However, what I have also always noticed in the past with a different
> protein-ligand,  and in these days, playing in VMD shows that the
> ligand left the protein, entering surrounding water, much before. NAMD
> did not stop at ligand entering the surrounding water and forces on
> ligand continued, pushing it to the other side of the surrounding
> water, without touching the protein.
>
> francesco
>
>
> ---------- Forwarded message ----------
> From: Francesco Pietra <chiendarret_at_gmail.com>
> Date: Tue, Apr 5, 2011 at 10:11 AM
> Subject: namd-l: Wrong exit from RAMD runs
> To: NAMD <namd-l_at_ks.uiuc.edu>
>
>
> 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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