RE: Fwd: RAMD Setting parameter TclForces from script failed

From: Cojocaru, Vlad (vlad.cojocaru_at_mpi-muenster.mpg.de)
Date: Mon Mar 28 2011 - 16:55:44 CDT

Francesco,

Of course Jim is right as well .. Why do you source your tcl scripts in the
.bashrc ? I don't understand how namd would automatically process your
.bashrc file ... Maybe I am missing something here ...

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: Jim Phillips [mailto:jim_at_ks.uiuc.edu]
Sent: Mon 3/28/2011 23:49
To: Francesco Pietra
Cc: Cojocaru, Vlad; NAMD
Subject: Re: Fwd: namd-l: RAMD Setting parameter TclForces from script failed
 

I'm assuming you aren't actually sourcing tcl code in your .bashrc. In
any case I would definitely only do this inside the NAMD config file
before any run commands.

-Jim

On Mon, 28 Mar 2011, Francesco Pietra wrote:

> I beg pardon again. My .bashrc contains
>
> # For RAMD in NAMD
> source /usr/local/namd_2.8nb/lib/ramd/scripts/ramd-4.1.tcl
>
>
>
> In turn, the ramd portion of namd conf file, which come after the
> "run" command, contains again
>
> #*** Random Acceleration Molecular Dynamics
> *************************************
>
> source /usr/local/namd_2.8nb/lib/ramd/scripts/ramd-4.1.tcl
>
> Does that result in having "tclforces on" after the "run" command?
> I'll try to delete the second source.
>
> f.
>
>
>
>
>
>
> ---------- Forwarded message ----------
> From: Francesco Pietra <chiendarret_at_gmail.com>
> Date: Mon, Mar 28, 2011 at 10:19 PM
> Subject: Fwd: namd-l: RAMD Setting parameter TclForces from script failed
> To: Jim Phillips <jim_at_ks.uiuc.edu>, "Cojocaru,Vlad"
> <vlad.cojocaru_at_mpi-muenster.mpg.de>, NAMD <namd-l_at_ks.uiuc.edu>
>
>
> Sorry I forgot both Vlad and the list.
>
>
> ---------- Forwarded message ----------
> From: Francesco Pietra <chiendarret_at_gmail.com>
> Date: Mon, Mar 28, 2011 at 10:17 PM
> Subject: Re: namd-l: RAMD Setting parameter TclForces from script failed
> To: Jim Phillips <jim_at_ks.uiuc.edu>
>
>
> On Mon, Mar 28, 2011 at 9:33 PM, Jim Phillips <jim_at_ks.uiuc.edu> wrote:
>>
>> It looks like you have "tclForces on" after run or minimize in your config
>> file, so possibly your tclForces script was not active during the RAMD run
>> at all.
>
> Hi  Jim:
> Yes, "tclforces on" is in the sourced ramd script, which comes after
> the "run" command in namd conf file.  I had checked that against namd
> 2.7 with external namd: there was the same order of statements.
>
> Now, if "tclforces on" is located in namd conf file, at the top:
>
>
> # forcefield
> paratypecharmm on
> parameters ./par_all27_prot_lipid.prm
> parameters ./AP1.r.prm
> tclForces on
>
> the error is:
>
> Info: Configuration file is ramd_acc-03.conf
> Info: Working in the current directory
> /home/francesco/work_hasic1a_GLUP_ASPP_allHSP_S-S/9.ramd_04-1.1
> TCL: Suspending until startup complete.
> ERROR: 'tclForcesScript' is a required configuration option
> ERROR:   when 'tclForces' is set
> ERROR: tclForcesScript defines:   Tcl script for global forces
> FATAL ERROR: ERROR(S) IN THE CONFIGURATION FILE
>
>
>
> Where should "tclforces on" be now located?
>
> thanks
> francesco
>
>
>
>>
>> -Jim
>>
>> On Mon, 28 Mar 2011, 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!
>>> **************************
>>>
>>
>

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