Re: RAMD Setting parameter TclForces from script failed

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Mon Mar 28 2011 - 09:50:31 CDT

Vlad:
In the old namd simulation from external ramd scripts, the log file
started by stating ramd presence and ended with seemingly fatal,
though irrelevant errors:

FIRST PART OF LOG:
Info: NONBONDED TABLE SIZE: 769 POINTS
TCL: RAMD:
TCL: RAMD: -------------------------------------------------------------------
TCL: RAMD: Random Acceleration Molecular Dynamics Simulation version 4.1
TCL: RAMD: -------------------------------------------------------------------
TCL: RAMD:
TCL: RAMD: mdSteps = 0
TCL: RAMD: accel = 0.1
TCL: RAMD: ramdSeed = 14257
TCL: RAMD: forceOutFreq = 50
TCL: RAMD: maxDist = 50
TCL: RAMD: firstProtAtom = 1
TCL: RAMD: rMinRamd = 0.02
TCL: RAMD: debugLevel = 0
TCL: RAMD: mdStart = no
TCL: RAMD: ramdSteps = 50
TCL: RAMD: firstRamdAtom = 2533
TCL: RAMD: lastRamdAtom = 2534
TCL: RAMD: lastProtAtom = 2532
TCL: RAMD: Pure RAMD simulation is performed
TCL: RAMD:
TCL: RAMD: Atoms subject to the random acceleration are: 2533 2534
Info: Startup phase 7 took 0.128011 s, 19.0119 MB of memory in use
Info: Startup phase 8 took 0.000475883 s, 19.769 MB of memory in use
Info: Finished startup at 19.831 s, 19.769 MB of memory in use

TCL: RAMD: 0 ***** INITIALIZE RAMD SIMULATION *****
TCL: RAMD: 0 >>> minimum travelled distance (A): 0.02
TCL: RAMD: 0 >>> minimum velocity (A/fs): 0.0004
TCL: RAMD: 0 >>> LIGAND COM IS: 9.85217805061 25.7175085064 7.7856016943
TCL: RAMD: 0 >>> PROTEIN COM IS: 7.11774674867 21.5684570118 10.8686520655
TCL: RAMD: 0 >>> DISTANCE LIGAND COM - PPROTEIN COM IS: DIST = 5.84781518534
TCL: RAMD: 0 >>> INITIAL RANDOM DIRECTION: -0.438558549195
0.749649725121 -0.495672965325 :: ||r|| = 1.0
TCL: RAMD: 0 ***** START WITH 50 STEPS OF RAMD SIMULATION *****
PRESSURE: 0 109.931 82.9908 22.7373 82.9908 224.171 51.6353 22.7373
51.6353 129.822
GPRESSURE: 0 89.1506 47.0191 -92.9346 70.8307 326.474 78.5356 27.9022
35.7032 153.917
ETITLE: TS BOND ANGLE DIHED
IMPRP ELECT VDW BOUNDARY MISC
       KINETIC TOTAL TEMP POTENTIAL
  TOTAL3 TEMPAVG PRESSURE GPRESSURE
VOLUME PRESSAVG GPRESSAVG

LAST PART OF LOG:
FINISHED WRITING RESTART COORDINATES
TCL: EXIT: 158200 > MAX DISTANCE LIGAND COM - PROTEIN COM REACHED
TCL: EXIT: 158200 > LIGAND EXIT EVENT DETECTED: STOP SIMULATION
TCL: EXIT: 158200 > EXIT NAMD
TCL: error reading output from command: interrupted system call
FATAL ERROR: error reading output from command: interrupted system call
    while executing
"exec kill -9 $process"
    (in namespace eval "::RAMD" script line 9)
    invoked from within
"namespace eval ::RAMD {

 #***** Terminate NAMD if the ligand has exited from the protein
 if { $exitFlag == 1 } {
  print "EXIT: $timeStep > MAX DI..."
    (procedure "calcforces" line 2)
    invoked from within
"calcforces"
------------- Processor 0 Exiting: Called CmiAbort ------------
Reason: FATAL ERROR: error reading output from command: interrupted system call
    while executing
"exec kill -9 $process"
    (in namespace eval "::RAMD" script line 9)
    invoked from within
"namespace eval ::RAMD {

 #***** Terminate NAMD if the ligand has exited from the protein
 if { $exitFlag == 1 } {
  print "EXIT: $timeStep > MAX DI..."
    (procedure "calcforces" line 2)
    invoked from within
"calcforces"

Charmrun: error on request socket--
Socket closed before recv
********************************************************************

In present simulation there is no trace of RAMD in the log file, while
ramd-4.1.tcl is sourced both in the namd conf file and in my .bashrc
(REDUNDANT AND DELETING WITH ONE ANOTHER?)

source /usr/local/namd_2.8nb/lib/ramd/scripts/ramd-4.1.tcl

In the older ramd simulation the scripts were in my home and sourced as:

source /home/francesco/ramd-4.1/scripts/ramd-4.1.tcl

in the namd conf file (I can't remember if the script was also sourced
in my .bashrc).

The script
/usr/local/namd2.8nb/libramd/scripts/ramd.4.1.tcl (where "nb" stands
for "night-build" of a couple of weeks ago) is correct about
"tclforces on", while there is no "tclforces on" in the namd conf
file.

******************************
Unlike in the older ramd simulations, now there are colvars
restraints, as from the namd conf file:

Info: COLLECTIVE VARIABLES CALCULATION REQUESTED
Info: COLLECTIVE VARIABLES CONFIGURATION ./CLA-ligands_colvars_press01.in
Info: COLLECTIVE VARIABLES RESTART INFORMATION
./press-02.restart.colvars.state
Info: LANGEVIN DYNAMICS ACTIVE

*******************************

thanks

francesco

On Mon, Mar 28, 2011 at 3:45 PM, Vlad Cojocaru
<vlad.cojocaru_at_mpi-muenster.mpg.de> wrote:
> Francesco,
>
> I don't think I've seen this error before ..
> It would useful if you could dig out the discussion we had before about this
> exiting issue ... I only remember it vaguely ...
>
> Vlad
>
> On 03/28/2011 12:26 PM, Francesco Pietra wrote:
>>
>> Hi:
>> I carried out a trial RAMD simulation with namd.2.8 (from binary
>> Linux64) charmmff for a protein-organic-ligand in a lipidic membrane.
>>
>> The simulation ended correctly at the bare 100 chosen steps, the
>> ligand did not move - as expected from 1000 steps  acc 0.3 ts 1fs.
>> Everything seems OK except the error below. I vaguely remember that
>> Vlad warned me in the past to compile namd in order that ramd exists
>> correctly. Was that the same errior message or anything new about
>> which I should now care?
>>
>> thanks
>> francesco pietra
>>
>> **************************
>>
>> ENERGY:    1000     10573.6218     17958.2104      9301.2411
>> 779.3272        -763083.0117     55270.6864         0.0000
>> 1.9652    144208.1552        -524989.8044       308.8680
>> -669197.9596   -524727.0908       309.0692           -173.1971
>> -32.1881   2166358.3052       -35.4825       -31.7813
>>
>> WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 1000
>> WRITING COORDINATES TO DCD FILE AT STEP 1000
>> WRITING COORDINATES TO RESTART FILE AT STEP 1000
>> FINISHED WRITING RESTART COORDINATES
>> The last position output (seq=1000) takes 0.134 seconds, 744.610 MB of
>> memory in use
>> WRITING VELOCITIES TO RESTART FILE AT STEP 1000
>> FINISHED WRITING RESTART VELOCITIES
>> The last velocity output (seq=1000) takes 0.021 seconds, 744.609 MB of
>> memory in use
>> TCL: Setting parameter TclForces to on
>> FATAL ERROR: Setting parameter TclForces from script failed!
>>
>> FATAL ERROR: Setting parameter TclForces from script failed!
>>
>> ------------- Processor 1 Exiting: Called CmiAbort ------------
>> Reason: FATAL ERROR: Setting parameter TclForces from script failed!
>>
>>
>> FATAL ERROR: Setting parameter TclForces from script failed!
>>
>> ------------- Processor 3 Exiting: Called CmiAbort ------------
>> Reason: FATAL ERROR: Setting parameter TclForces from script failed!
>>
>>
>> ------------- Processor 0 Exiting: Called CmiAbort ------------
>> Reason: FATAL ERROR: Setting parameter TclForces from script failed!
>>
>>
>> FATAL ERROR: Setting parameter TclForces from script failed!
>>
>> ------------- Processor 2 Exiting: Called CmiAbort ------------
>> Reason: FATAL ERROR: Setting parameter TclForces from script failed!
>> **************************
>>
>>
>
> --
> 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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