From: Cojocaru, Vlad (vlad.cojocaru_at_mpi-muenster.mpg.de)
Date: Mon Mar 28 2011 - 14:20:56 CDT
Hi Francesco,
This looks strange ... I remember at the beginning of namd 2.7 there was a
bug in NAMD (not in the RAMD) which initialized Alchemical simulations for
some reason ... After this was fixed, the RAMD scripts worked fine ... Now,
it is possible that there is a similar bug in namd 2.8 which initializes for
some reason the colvar module ...
I suggest the following:
run RAMD with the stable version namd 2.7 ... if this works well, it means
that the problem is somewhere in the namd 2.8 ... or in the communication
between namd 2.8 and tcl.
Did you test that tcl forces work properly in namd 2.8 ? If not, I suggest to
run 1 short tutorial to make sure that your tcl forces work OK ...
With what version of tcl did you compile namd 2.8 ?
The RAMD scripts have not been changed since their incorporation in the NAMD
CVS ...
Let me know if they work with namd 2.7 ... Then, after I install namd 2.8 at
my site here, maybe I find the time to do a short test ...
Best
Vlad
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
-----Original Message-----
From: owner-namd-l_at_ks.uiuc.edu on behalf of Francesco Pietra
Sent: Mon 3/28/2011 16:50
To: Cojocaru, Vlad
Cc: NAMD
Subject: Re: namd-l: RAMD Setting parameter TclForces from script failed
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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