Re: Fwd: Wrong exit from RAMD runs

From: Jim Phillips (jim_at_ks.uiuc.edu)
Date: Wed Apr 13 2011 - 10:02:18 CDT

On second thought, this might not work from inside calcforces. -Jim

On Wed, 13 Apr 2011, Jim Phillips wrote:

>
> 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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