Re: Fwd: Wrong exit from RAMD runs

From: Vlad Cojocaru (vlad.cojocaru_at_mpi-muenster.mpg.de)
Date: Thu Apr 14 2011 - 03:08:54 CDT

Jim,

As I recall I had a problem with using "exit" and that's why I changed
it to "exec kill -9 $process" ..
Do not remember exactly how it was but I have run the scripts with the
"exec" command for quite a while and they have always exited clean.

Vlad

On 04/13/2011 05:02 PM, Jim Phillips wrote:
>
> 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
>>

-- 
Dr. Vlad Cojocaru
Max Planck Institute for Molecular Biomedicine
Department of Cellular and Developmental Biology
Roentgenstrasse 20
48149 Muenster, Germany
tel: +49-251-70365-324
fax: +49-251-70365-399
email: vlad.cojocaru[at]mpi-muenster.mpg.de

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