From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Mon Mar 28 2011 - 14:43:34 CDT
Hi Vlad: It seems that checking tcl forces is what should be done
first. Please see below
On Mon, Mar 28, 2011 at 9:20 PM, Cojocaru, Vlad
<vlad.cojocaru_at_mpi-muenster.mpg.de> wrote:
> 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 ...
The colvars are deliberately there, and must be activated.
>
> 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.
I don't know if 2.7 works with present colvars. Has 2.7 ramd scripts
inside? It had none when I worked with 2.7.
>
> 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 ...
Could you give a reference on how-to-do that?
>
> With what version of tcl did you compile namd 2.8 ?
I don't know which version the developers used. How to check from the
binary the tcl version?
I used the GNU/Linux 64 binary (compiled on RedHat probably) on Debian
amd64. I never attempted to compile namd. Do you have a protocol for
Linux? Take into account please that I am an experimental organic
chemist ...
That said, I do not rule out entirely that I did a mistake in the namd
conf file. At a new control I could not detect any anomaly. It is
strange, however, that in spite of "binaryoutput no" in namd
conf file, with the ramd module included, no pdb file In the extension
.coor comes out ; only binary ..restart.coor is obtained. In the
absence of ramd I got both.
thanks
francesco
>
> 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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